Variant report

Variant	rs2259571
Chromosome Location	chr6:31583827-31583828
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:55)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:55 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr6:31583473-31583967	GM12878	blood:	n/a	n/a
2	TBP	chr6:31583577-31583935	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:31583606-31583893	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:31583355-31584499	HL-60	blood:	n/a	n/a
5	STAT3	chr6:31583739-31583838	GM12878	blood:	n/a	n/a
6	MAFK	chr6:31583666-31583851	K562	blood:	n/a	n/a
7	POLR2A	chr6:31583561-31583866	GM12878	blood:	n/a	n/a
8	MAFK	chr6:31583712-31583992	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:31583491-31584030	GM12891	blood:	n/a	n/a
10	PML	chr6:31583345-31584066	GM12878	blood:	n/a	n/a
11	MTA3	chr6:31582754-31584475	GM12878	blood:	n/a	n/a
12	TAF1	chr6:31583597-31584057	GM12878	blood:	n/a	n/a
13	MYC	chr6:31583457-31583970	NB4	blood:	n/a	n/a
14	POLR2A	chr6:31583565-31583908	GM12878	blood:	n/a	n/a
15	TBL1XR1	chr6:31583601-31583877	GM12878	blood:	n/a	n/a
16	MAX	chr6:31583540-31583935	K562	blood:	n/a	n/a
17	POLR2A	chr6:31583570-31583990	GM12891	blood:	n/a	n/a
18	SPI1	chr6:31583250-31584224	GM12878	blood:	n/a	chr6:31583252-31583259
19	TAF1	chr6:31583585-31583906	GM12891	blood:	n/a	n/a
20	MAFF	chr6:31583765-31583956	K562	blood:	n/a	n/a
21	EP300	chr6:31583566-31583882	GM12878	blood:	n/a	n/a
22	SPI1	chr6:31583423-31584118	GM12891	blood:	n/a	n/a
23	RUNX3	chr6:31583357-31584136	GM12878	blood:	n/a	n/a
24	RUNX3	chr6:31583322-31584188	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:31583544-31584030	GM12891	blood:	n/a	n/a
26	SP1	chr6:31583545-31583893	GM12878	blood:	n/a	n/a
27	SPI1	chr6:31583535-31583857	K562	blood:	n/a	n/a
28	CHD2	chr6:31583517-31583944	GM12878	blood:	n/a	n/a
29	POLR2A	chr6:31583382-31584137	GM12878	blood:	n/a	n/a
30	MAFF	chr6:31583790-31584012	HepG2	liver:	n/a	n/a
31	ELK1	chr6:31583702-31583973	GM12878	blood:	n/a	n/a
32	MAZ	chr6:31583530-31583923	GM12878	blood:	n/a	n/a
33	SPI1	chr6:31583541-31583938	GM12878	blood:	n/a	n/a
34	SPI1	chr6:31583424-31583977	HL-60	blood:	n/a	n/a
35	POU2F2	chr6:31583546-31584084	GM12891	blood:	n/a	n/a
36	REST	chr6:31583454-31584106	HL-60	blood:	n/a	n/a
37	CTCF	chr6:31583720-31583870	GM12873	blood:	n/a	n/a
38	MAFK	chr6:31583722-31583948	HepG2	liver:	n/a	n/a
39	STAT5A	chr6:31583382-31583950	GM12878	blood:	n/a	n/a
40	SPI1	chr6:31583324-31584268	HL-60	blood:	n/a	n/a
41	SPI1	chr6:31583448-31583994	GM12891	blood:	n/a	n/a
42	YY1	chr6:31583666-31583940	GM12878	blood:	n/a	n/a
43	RCOR1	chr6:31583514-31584005	GM12878	blood:	n/a	n/a
44	IKZF1	chr6:31583553-31583878	GM12878	blood:	n/a	n/a
45	STAT5A	chr6:31583647-31583999	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:31583657-31584058	NB4	blood:	n/a	n/a
47	ELF1	chr6:31583463-31584180	GM12878	blood:	n/a	n/a
48	POLR2A	chr6:31583354-31584619	HL-60	blood:	n/a	n/a
49	POLR2A	chr6:31583020-31584009	SK-N-MC	brain:	n/a	n/a
50	MTA3	chr6:31583513-31584216	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31513771..31519008-chr6:31582734..31585702,4	K562	blood:
2	chr6:31539772..31542619-chr6:31581316..31584667,3	K562	blood:
3	chr6:31515338..31517420-chr6:31583462..31585517,2	MCF-7	breast:
4	chr6:31578073..31580095-chr6:31581694..31583880,2	MCF-7	breast:
5	chr6:31510094..31511838-chr6:31582401..31584650,2	K562	blood:
6	chr6:31513234..31515924-chr6:31582326..31585070,2	K562	blood:

No data

Variant related genes	Relation type
PRRC2A	TF binding region
UQCRHP1	TF binding region
ENSG00000204498	Chromatin interaction
ENSG00000226979	Chromatin interaction
ENSG00000230622	Chromatin interaction
ENSG00000213760	Chromatin interaction
ENSG00000254870	Chromatin interaction
ENSG00000234006	Chromatin interaction
ENSG00000198563	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1052486	0.87[ASN][1000 genomes]
rs1077393	0.87[ASN][1000 genomes]
rs13716	0.87[AMR][1000 genomes]
rs2051552	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2077491	0.85[ASN][1000 genomes]
rs2242660	0.80[ASN][1000 genomes]
rs2260000	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2260050	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2507957	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2736155	0.84[ASN][1000 genomes]
rs2736171	0.87[EUR][1000 genomes]
rs2736172	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2736176	0.87[AMR][1000 genomes]
rs2736178	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844472	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844475	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2844476	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844477	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2857693	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2857694	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2857697	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2857698	0.91[AMR][1000 genomes]
rs3091280	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3135044	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3993747	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5872	0.82[AMR][1000 genomes]
rs707919	0.82[AMR][1000 genomes]
rs755714	0.87[AMR][1000 genomes]
rs7765613	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805262	0.93[ASN][1000 genomes]
rs805299	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
13	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS 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	326 gene(s)	inside rSNPs	diseases
14	nsv462871	chr6:31575276-31632134	Strong transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	133 gene(s)	inside rSNPs	diseases
15	nsv601942	chr6:31575276-31632134	Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	133 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2259571	AIF1	Cis_1M	lymphoblastoid	RTeQTL
rs2259571	HLA-DQB1	Cis_chr	lymphoblastoid	RTeQTL
rs2259571	CSNK2B	cis	lymphoblastoid	seeQTL
rs2259571	CSNK2B	Cis_1M	lymphoblastoid	RTeQTL
rs2259571	PRRC2A	cis	lymphoblastoid	seeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31581400-31585200	Enhancers	Primary B cells from peripheral blood	blood
2	chr6:31581800-31584400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr6:31582000-31584000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:31582000-31584200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr6:31582000-31584200	Enhancers	H9 Cell Line	embryonic stem cell
6	chr6:31582000-31584800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr6:31582000-31585200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:31582200-31584200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr6:31582200-31584200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:31582200-31584400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:31582200-31584400	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr6:31582200-31584400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr6:31582200-31585000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:31582200-31587800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:31582600-31584000	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr6:31582600-31584400	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr6:31582600-31584400	Flanking Active TSS	Fetal Thymus	thymus
18	chr6:31582600-31584800	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr6:31582800-31584000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:31582800-31584000	Enhancers	Fetal Lung	lung
21	chr6:31582800-31584200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr6:31582800-31584200	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr6:31582800-31584400	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr6:31583000-31584200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:31583000-31584200	Active TSS	Adipose Nuclei	Adipose
26	chr6:31583000-31584200	Active TSS	Fetal Muscle Trunk	muscle
27	chr6:31583000-31584400	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr6:31583000-31584400	Active TSS	Brain Substantia Nigra	brain
29	chr6:31583000-31584400	Active TSS	Fetal Muscle Leg	muscle
30	chr6:31583000-31584600	Active TSS	Placenta	Placenta
31	chr6:31583000-31584800	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr6:31583000-31584800	Flanking Active TSS	Dnd41	blood
33	chr6:31583000-31585000	Enhancers	K562	blood
34	chr6:31583000-31587200	Weak transcription	Colonic Mucosa	Colon
35	chr6:31583000-31587600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr6:31583200-31584000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:31583200-31584000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr6:31583200-31584200	Active TSS	Duodenum Mucosa	Duodenum
39	chr6:31583200-31584200	Flanking Active TSS	Thymus	Thymus
40	chr6:31583200-31584400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:31583200-31584600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr6:31583400-31584000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:31583400-31584000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:31583400-31584200	Active TSS	Liver	Liver
45	chr6:31583400-31584200	Active TSS	Fetal Intestine Large	intestine
46	chr6:31583400-31584400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr6:31583400-31584400	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr6:31583400-31584600	Active TSS	Brain Hippocampus Middle	brain
49	chr6:31583400-31584800	Enhancers	HepG2	liver
50	chr6:31583600-31584000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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