Variant report

Variant	rs2251824
Chromosome Location	chr6:31511857-31511858
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HNF4A	chr6:31511440-31511899	HepG2	liver:	n/a	n/a

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31508088..31512302-chr6:31792582..31797881,5	K562	blood:
2	chr6:31510898..31512528-chr6:31621703..31624538,2	MCF-7	breast:
3	chr6:31508752..31512657-chr6:31701865..31705930,6	K562	blood:
4	chr6:31509573..31511941-chr6:31658992..31661656,2	K562	blood:
5	chr6:31506561..31512642-chr6:31697539..31702106,5	K562	blood:
6	chr6:31510366..31512427-chr6:31782713..31784420,2	K562	blood:
7	chr6:31507451..31516055-chr6:31617949..31624791,11	MCF-7	breast:
8	chr6:31510807..31512542-chr6:31620152..31621684,2	MCF-7	breast:
9	chr6:31511781..31517209-chr6:31545410..31553496,14	K562	blood:
10	chr6:31506496..31512275-chr6:31630248..31634828,11	K562	blood:
11	chr6:31510116..31512657-chr6:31703324..31705930,3	K562	blood:
12	chr6:31510463..31512638-chr6:31684771..31686477,2	MCF-7	breast:
13	chr6:31506740..31512488-chr6:31586502..31592966,30	K562	blood:
14	chr6:31506595..31512441-chr6:31585525..31590767,30	K562	blood:
15	chr6:31510286..31512313-chr6:31556327..31558851,2	K562	blood:
16	chr6:31511829..31516829-chr6:31586761..31590434,8	MCF-7	breast:
17	chr6:31510287..31512759-chr6:31568800..31571526,2	K562	blood:
18	chr6:31458384..31468965-chr6:31503613..31512721,28	K562	blood:
19	chr6:31509610..31511925-chr6:31559593..31562422,2	K562	blood:
20	chr6:31508169..31513281-chr6:31547465..31550370,6	K562	blood:
21	chr6:31507406..31516955-chr6:31615847..31623354,26	K562	blood:
22	chr6:31505350..31512312-chr6:31630543..31635379,11	K562	blood:
23	chr6:31509522..31512324-chr6:31604128..31605952,2	K562	blood:
24	chr6:31460486..31468205-chr6:31503942..31512721,23	K562	blood:
25	chr6:31511090..31513028-chr6:31593636..31596148,2	K562	blood:
26	chr6:31509889..31512472-chr6:31802635..31805585,2	MCF-7	breast:

No data

Variant related genes	Relation type
NFKBIL1	TF binding region
SNORD84	TF binding region
DDX39B	TF binding region
ENSG00000204388	Chromatin interaction
ENSG00000263020	Chromatin interaction
ENSG00000201680	Chromatin interaction
ENSG00000204469	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000204420	Chromatin interaction
ENSG00000204390	Chromatin interaction
ENSG00000204516	Chromatin interaction
ENSG00000204387	Chromatin interaction
ENSG00000213722	Chromatin interaction
ENSG00000200816	Chromatin interaction
ENSG00000227507	Chromatin interaction
ENSG00000201754	Chromatin interaction
ENSG00000204389	Chromatin interaction
ENSG00000204475	Chromatin interaction
ENSG00000201823	Chromatin interaction
ENSG00000204427	Chromatin interaction
ENSG00000204463	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000201207	Chromatin interaction
ENSG00000204444	Chromatin interaction
ENSG00000213719	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12663590	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1800630	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2255899	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2259435	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2429642	1.00[ASN][1000 genomes]
rs2516395	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516397	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516478	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516489	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523499	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523501	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523512	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2534652	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2534653	0.99[ASN][1000 genomes]
rs2734586	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857706	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2251824	HIST1H2AM	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31510600-31513200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:31510600-31513200	Weak transcription	Ovary	ovary
3	chr6:31510600-31513600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:31510600-31514200	Weak transcription	Aorta	Aorta
5	chr6:31510600-31514600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:31510600-31514600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:31510600-31515800	Weak transcription	Gastric	stomach
8	chr6:31510800-31513200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:31510800-31513200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:31510800-31513600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:31510800-31513800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:31510800-31514400	Weak transcription	Right Atrium	heart
13	chr6:31510800-31514600	Weak transcription	Small Intestine	intestine
14	chr6:31510800-31515400	Weak transcription	Lung	lung
15	chr6:31511000-31513000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:31511000-31513000	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:31511000-31513200	Weak transcription	NHLF	lung
18	chr6:31511000-31513600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:31511000-31513600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:31511000-31513600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:31511000-31513600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:31511000-31513800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:31511000-31513800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr6:31511000-31513800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:31511000-31513800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:31511000-31513800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:31511000-31513800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr6:31511000-31513800	Weak transcription	Fetal Intestine Large	intestine
29	chr6:31511000-31513800	Weak transcription	Fetal Lung	lung
30	chr6:31511000-31513800	Weak transcription	Fetal Stomach	stomach
31	chr6:31511000-31513800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr6:31511000-31513800	Weak transcription	Osteobl	bone
33	chr6:31511000-31514000	Weak transcription	Primary T cells from cord blood	blood
34	chr6:31511000-31514000	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr6:31511000-31514000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:31511000-31514200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr6:31511000-31514200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:31511000-31514200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr6:31511000-31514200	Weak transcription	Adipose Nuclei	Adipose
40	chr6:31511000-31514200	Weak transcription	Placenta	Placenta
41	chr6:31511000-31514200	Weak transcription	Thymus	Thymus
42	chr6:31511000-31514400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr6:31511000-31514400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:31511000-31514400	Weak transcription	Spleen	Spleen
45	chr6:31511000-31514600	Weak transcription	Right Ventricle	heart
46	chr6:31511200-31512600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr6:31511200-31513000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr6:31511200-31513000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr6:31511200-31513000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:31511200-31513000	Weak transcription	Brain Cingulate Gyrus	brain

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