Variant report

Variant	rs2523504
Chromosome Location	chr6:31510858-31510859
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:47)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31508687-31511132	K562	blood:	n/a	n/a
2	FOXA1	chr6:31510822-31511418	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:31508618-31511594	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:31508784-31510863	K562	blood:	n/a	n/a
5	HEY1	chr6:31508765-31511176	K562	blood:	n/a	n/a
6	NR2F2	chr6:31508474-31511071	K562	blood:	n/a	n/a
7	FOXA1	chr6:31510738-31511412	HepG2	liver:	n/a	n/a
8	POLR2A	chr6:31508749-31510965	K562	blood:	n/a	n/a
9	POLR2A	chr6:31505819-31511508	SK-N-MC	brain:	n/a	n/a
10	HCFC1	chr6:31508564-31511015	Hela-S3	cervix:	n/a	n/a
11	MXI1	chr6:31507514-31511487	SK-N-SH	brain:	n/a	n/a
12	REST	chr6:31509207-31510885	PFSK-1	brain:	n/a	chr6:31510328-31510337 chr6:31510323-31510343
13	POLR2A	chr6:31507792-31511234	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr6:31507733-31511078	PFSK-1	brain:	n/a	n/a

No data

(count:47 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31508088..31512302-chr6:31792582..31797881,5	K562	blood:
2	chr6:31508602..31511012-chr6:31803135..31806104,3	K562	blood:
3	chr6:31508752..31512657-chr6:31701865..31705930,6	K562	blood:
4	chr6:31509573..31511941-chr6:31658992..31661656,2	K562	blood:
5	chr6:31509627..31511469-chr6:31626737..31628735,4	MCF-7	breast:
6	chr6:31507082..31511713-chr6:31583957..31591905,17	MCF-7	breast:
7	chr6:31506561..31512642-chr6:31697539..31702106,5	K562	blood:
8	chr6:31510366..31512427-chr6:31782713..31784420,2	K562	blood:
9	chr6:31507451..31516055-chr6:31617949..31624791,11	MCF-7	breast:
10	chr6:31510807..31512542-chr6:31620152..31621684,2	MCF-7	breast:
11	chr6:31508352..31511076-chr6:31794765..31796870,2	MCF-7	breast:
12	chr6:31506496..31512275-chr6:31630248..31634828,11	K562	blood:
13	chr6:31459710..31467567-chr6:31506191..31511027,18	MCF-7	breast:
14	chr6:31508667..31511581-chr6:31742885..31745171,3	MCF-7	breast:
15	chr6:31510116..31512657-chr6:31703324..31705930,3	K562	blood:
16	chr6:31510463..31512638-chr6:31684771..31686477,2	MCF-7	breast:
17	chr6:31508080..31511338-chr6:31773122..31775825,3	K562	blood:
18	chr6:31506740..31512488-chr6:31586502..31592966,30	K562	blood:
19	chr6:31510094..31511838-chr6:31582401..31584650,2	K562	blood:
20	chr6:31509079..31511785-chr6:31559160..31560764,2	MCF-7	breast:
21	chr6:31508345..31511059-chr6:31794031..31797026,5	K562	blood:
22	chr6:31508732..31511014-chr6:31781931..31784408,2	K562	blood:
23	chr6:31510269..31511789-chr8:128582213..128583733,2	K562	blood:
24	chr6:31506595..31512441-chr6:31585525..31590767,30	K562	blood:
25	chr6:31508417..31511292-chr6:31625631..31629953,4	K562	blood:
26	chr6:31508578..31511041-chr6:31743489..31745514,2	K562	blood:
27	chr6:31509573..31511196-chr6:31578119..31580506,2	K562	blood:
28	chr6:31510286..31512313-chr6:31556327..31558851,2	K562	blood:
29	chr6:31510287..31512759-chr6:31568800..31571526,2	K562	blood:
30	chr6:31509091..31511742-chr6:31868193..31871571,3	MCF-7	breast:
31	chr6:31507205..31511686-chr6:31618024..31622039,13	K562	blood:
32	chr6:31458384..31468965-chr6:31503613..31512721,28	K562	blood:
33	chr6:31509610..31511925-chr6:31559593..31562422,2	K562	blood:
34	chr6:31507998..31511841-chr6:31541735..31545245,5	MCF-7	breast:
35	chr6:31508169..31513281-chr6:31547465..31550370,6	K562	blood:
36	chr6:31507406..31516955-chr6:31615847..31623354,26	K562	blood:
37	chr6:31507927..31511187-chr6:31633283..31638231,4	MCF-7	breast:
38	chr6:31505350..31512312-chr6:31630543..31635379,11	K562	blood:
39	chr6:31506029..31511048-chr6:31626239..31630287,7	MCF-7	breast:
40	chr6:31507058..31511692-chr6:31586700..31590601,11	MCF-7	breast:
41	chr6:31509522..31512324-chr6:31604128..31605952,2	K562	blood:
42	chr6:31462628..31467072-chr6:31508179..31511597,8	MCF-7	breast:
43	chr6:31508700..31511164-chr6:32162690..32164850,2	K562	blood:
44	chr6:31460486..31468205-chr6:31503942..31512721,23	K562	blood:
45	chr6:31504619..31510971-chr6:31539361..31543067,6	K562	blood:
46	chr6:31507944..31511146-chr6:31743964..31746169,3	K562	blood:
47	chr6:31509889..31512472-chr6:31802635..31805585,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NFKBIL1-7	chr6:31510482-31510904	ENSG00000234006.1
2	lnc-NFKBIL1-7	chr6:31510486-31510915	ENSG00000234006.1

No data

Variant related genes	Relation type
NFKBIL1	TF binding region
SNORD84	TF binding region
DDX39B	TF binding region
ENSG00000204444	Chromatin interaction
ENSG00000204394	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000232810	Chromatin interaction
ENSG00000201207	Chromatin interaction
ENSG00000230622	Chromatin interaction
ENSG00000204389	Chromatin interaction
ENSG00000201754	Chromatin interaction
ENSG00000204366	Chromatin interaction
ENSG00000240053	Chromatin interaction
ENSG00000204420	Chromatin interaction
ENSG00000213722	Chromatin interaction
ENSG00000204516	Chromatin interaction
ENSG00000201823	Chromatin interaction
ENSG00000204472	Chromatin interaction
ENSG00000204463	Chromatin interaction
ENSG00000201680	Chromatin interaction
ENSG00000204396	Chromatin interaction
ENSG00000227198	Chromatin interaction
ENSG00000204427	Chromatin interaction
ENSG00000204387	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000227507	Chromatin interaction
ENSG00000204390	Chromatin interaction
ENSG00000204392	Chromatin interaction
ENSG00000204469	Chromatin interaction
ENSG00000204439	Chromatin interaction
ENSG00000213719	Chromatin interaction
ENSG00000213654	Chromatin interaction
ENSG00000263020	Chromatin interaction
ENSG00000204388	Chromatin interaction
ENSG00000204301	Chromatin interaction
ENSG00000226979	Chromatin interaction
ENSG00000166278	Chromatin interaction
ENSG00000204475	Chromatin interaction
ENSG00000200816	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1055388	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2075580	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2075582	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2239525	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239526	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523507	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2857605	0.96[ASN][1000 genomes]
rs3130055	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs933208	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
2	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
3	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
4	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
5	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
6	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
7	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
8	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
9	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
10	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
11	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
12	nsv1018463	chr6:31337336-31525275	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
13	nsv538189	chr6:31337336-31525275	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
14	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
15	esv2757162	chr6:31353329-31542308	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
16	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
17	nsv432877	chr6:31412961-31528690	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
18	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
19	nsv470809	chr6:31496915-31544189	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2523504	HLA-C	cis	Whole Blood	GTEx
rs2523504	XXbac-BPG248L24.12	cis	Adipose Subcutaneous	GTEx
rs2523504	HIST1H1B	cis	cerebellum	SCAN
rs2523504	XXbac-BPG248L24.12	cis	Artery Tibial	GTEx
rs2523504	HLA-DRB5	cis	lymphoblastoid	GTEx
rs2523504	XXbac-BPG248L24.12	cis	lung	GTEx
rs2523504	HLA-C	cis	lymphoblastoid	GTEx
rs2523504	XXbac-BPG248L24.12	cis	Thyroid	GTEx
rs2523504	XXbac-BPG248L24.12	cis	Whole Blood	GTEx
rs2523504	XXbac-BPG248L24.12	cis	Skin Sun Exposed Lower leg	GTEx
rs2523504	XXbac-BPG248L24.12	cis	Muscle Skeletal	GTEx
rs2523504	HLA-B	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31508000-31511600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:31508200-31511000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:31508200-31511000	Active TSS	NHLF	lung
4	chr6:31508200-31511400	Active TSS	GM12878-XiMat	blood
5	chr6:31508400-31511000	Active TSS	H1 Cell Line	embryonic stem cell
6	chr6:31508400-31511000	Active TSS	H9 Cell Line	embryonic stem cell
7	chr6:31508400-31511000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:31508400-31511000	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr6:31508400-31511000	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr6:31508400-31511000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:31508400-31511000	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr6:31508400-31511000	Active TSS	Left Ventricle	heart
13	chr6:31508400-31511000	Active TSS	Sigmoid Colon	Sigmoid Colon
14	chr6:31508400-31511000	Active TSS	HSMMtube	muscle
15	chr6:31508400-31511200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:31508400-31511200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:31508400-31511600	Active TSS	Psoas Muscle	Psoas
18	chr6:31508600-31511000	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr6:31508600-31511000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:31508600-31511000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:31508600-31511000	Active TSS	Brain Anterior Caudate	brain
22	chr6:31508600-31511000	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr6:31508600-31511200	Active TSS	Colonic Mucosa	Colon
24	chr6:31508800-31511000	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr6:31508800-31511000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:31509000-31511000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:31509000-31511000	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr6:31509000-31511000	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr6:31509000-31511200	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr6:31509000-31511200	Active TSS	A549	lung
31	chr6:31509000-31511600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:31509400-31511400	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr6:31510000-31511200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr6:31510200-31511000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:31510200-31511000	Flanking Active TSS	Fetal Brain Female	brain
36	chr6:31510200-31511000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr6:31510200-31511000	Flanking Active TSS	HUVEC	blood vessel
38	chr6:31510200-31511200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr6:31510400-31511000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr6:31510400-31511000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr6:31510400-31511000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr6:31510400-31511000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr6:31510400-31511000	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr6:31510400-31511000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr6:31510400-31511000	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr6:31510400-31511000	Flanking Active TSS	HSMM	muscle
47	chr6:31510400-31511200	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr6:31510600-31511000	Enhancers	Primary T cells from cord blood	blood
49	chr6:31510600-31511000	Enhancers	Primary T cells fromperipheralblood	blood
50	chr6:31510600-31511000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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