Variant report

Variant	rs11544238
Chromosome Location	chr12:57870155-57870156
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT1	chr12:57869994-57870262	GM12878	blood:	n/a	chr12:57870061-57870073
2	POLR2A	chr12:57870030-57870491	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:57870073-57870456	GM15510	blood:	n/a	n/a
4	CHD1	chr12:57869717-57870571	GM12878	blood:	n/a	n/a
5	CTCF	chr12:57870020-57870170	SAEC	small airway:	n/a	n/a
6	POLR2A	chr12:57869989-57870509	GM12891	blood:	n/a	n/a
7	POLR2A	chr12:57869742-57870426	GM12878	blood:	n/a	n/a
8	MAX	chr12:57868611-57870538	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr12:57870060-57870210	AG04449	skin:	n/a	n/a
10	CTCF	chr12:57870120-57870270	GM12873	blood:	n/a	n/a
11	CTCF	chr12:57870120-57870270	GM12874	blood:	n/a	n/a
12	CTCF	chr12:57870059-57870257	GM20000	blood:	n/a	n/a
13	CTCF	chr12:57870140-57870290	GM06990	blood:	n/a	n/a
14	RAD21	chr12:57869943-57870329	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:57870102-57870560	GM12878	blood:	n/a	n/a
16	SRF	chr12:57870032-57870202	GM12878	blood:	n/a	chr12:57870077-57870087
17	CTCF	chr12:57870080-57870230	HMEC	breast:	n/a	n/a
18	CTCF	chr12:57870080-57870230	GM12878	blood:	n/a	n/a
19	ZEB1	chr12:57869391-57870479	GM12878	blood:	n/a	n/a
20	CTCF	chr12:57870120-57870270	GM12864	blood:	n/a	n/a
21	CTCF	chr12:57869994-57870469	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr12:57869921-57870534	GM12878	blood:	n/a	n/a
23	EGR1	chr12:57869968-57870245	GM12878	blood:	n/a	chr12:57870077-57870090 chr12:57870072-57870094 chr12:57870019-57870033 chr12:57870074-57870088 chr12:57870077-57870087 chr12:57870077-57870090
24	CTCF	chr12:57870084-57870441	Lung_OC	lung:	n/a	n/a
25	CTCF	chr12:57870120-57870270	GM12872	blood:	n/a	n/a
26	RCOR1	chr12:57869914-57870439	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:57869971-57870514	GM12878	blood:	n/a	n/a
28	RFX5	chr12:57870076-57870549	GM12878	blood:	n/a	chr12:57870532-57870541
29	CTCF	chr12:57870100-57870250	GM12866	blood:	n/a	n/a
30	SP1	chr12:57869947-57870356	GM12878	blood:	n/a	chr12:57870019-57870033
31	TAF1	chr12:57869990-57870372	GM12878	blood:	n/a	n/a
32	BHLHE40	chr12:57869531-57870501	GM12878	blood:	n/a	chr12:57870064-57870080
33	CTCF	chr12:57870100-57870250	HVMF	connective:	n/a	n/a
34	CTCF	chr12:57870100-57870250	HMF	breast:	n/a	n/a
35	CTCF	chr12:57870100-57870250	HPF	lung:	n/a	n/a
36	EBF1	chr12:57869763-57870327	GM12878	blood:	n/a	n/a
37	FOXM1	chr12:57869872-57870465	GM12878	blood:	n/a	n/a
38	CTCF	chr12:57869624-57870523	GM12891	blood:	n/a	n/a
39	CTCF	chr12:57870040-57870190	HRE	kidney:	n/a	n/a
40	CTCF	chr12:57870100-57870250	HCM	heart:	n/a	n/a
41	EGR1	chr12:57869895-57870236	GM12878	blood:	n/a	chr12:57870077-57870090 chr12:57870072-57870094 chr12:57870019-57870033 chr12:57870074-57870088 chr12:57870077-57870087 chr12:57870077-57870090
42	MXI1	chr12:57870018-57870496	GM12878	blood:	n/a	n/a
43	CTCF	chr12:57870110-57870192	A549	lung:	n/a	n/a
44	CTCF	chr12:57869694-57870571	GM12878	blood:	n/a	n/a
45	CTCF	chr12:57870047-57870265	GM10248	blood:	n/a	n/a
46	CTCF	chr12:57870036-57870283	GM13976	blood:	n/a	n/a
47	CTCF	chr12:57870040-57870190	SAEC	small airway:	n/a	n/a
48	CTBP2	chr12:57869110-57870427	H1-hESC	embryonic stem cell:	n/a	n/a
49	WRNIP1	chr12:57870032-57870344	GM12878	blood:	n/a	n/a
50	SMC3	chr12:57870039-57870396	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57869556..57871935-chr12:57881103..57884583,3	K562	blood:
2	chr12:57869564..57871597-chr12:57983396..57986014,2	K562	blood:
3	chr12:57856465..57858334-chr12:57867233..57870220,2	MCF-7	breast:

Variant related genes	Relation type
ARHGAP9	TF binding region
ENSG00000166986	Chromatin interaction
ENSG00000111087	Chromatin interaction
ENSG00000123329	Chromatin interaction
ENSG00000166908	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10783827	0.89[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap]
rs10783828	0.81[JPT][hapmap]
rs10876986	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2228224	0.91[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2228225	0.80[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2228226	0.81[JPT][hapmap]
rs2277316	0.81[JPT][hapmap]
rs2277317	0.81[JPT][hapmap]
rs2292657	0.96[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3782125	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3782126	0.80[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3817474	0.80[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3817475	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3825077	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4760148	0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4760255	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7309467	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][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	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers 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	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
10	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
12	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
14	nsv559035	chr12:57860972-57870648	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
15	nsv819597	chr12:57868561-57870210	Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11544238	ITGB7	cis	cerebellum	SCAN
rs11544238	ATF7	cis	cerebellum	SCAN
rs11544238	ITGA5	cis	cerebellum	SCAN
rs11544238	OR6C4	cis	parietal	SCAN
rs11544238	KIAA0748	cis	cerebellum	SCAN
rs11544238	DNAJC14	cis	cerebellum	SCAN
rs11544238	RDH5	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57859600-57870800	Weak transcription	A549	lung
2	chr12:57862800-57870400	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
3	chr12:57868600-57870600	Bivalent Enhancer	Fetal Heart	heart
4	chr12:57868800-57870200	Bivalent Enhancer	Fetal Brain Male	brain
5	chr12:57868800-57870200	Bivalent/Poised TSS	Fetal Brain Female	brain
6	chr12:57868800-57870400	Bivalent Enhancer	Fetal Lung	lung
7	chr12:57868800-57870800	Weak transcription	K562	blood
8	chr12:57869000-57870200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr12:57869000-57870200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:57869000-57870200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
11	chr12:57869000-57870200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:57869000-57870200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:57869000-57870200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:57869000-57870200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:57869000-57870400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
16	chr12:57869000-57870400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr12:57869000-57870400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr12:57869000-57870400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:57869000-57870400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:57869000-57870400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
21	chr12:57869000-57870400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
22	chr12:57869000-57870400	Flanking Active TSS	Right Ventricle	heart
23	chr12:57869000-57870400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
24	chr12:57869000-57870600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
25	chr12:57869000-57870600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
26	chr12:57869200-57870200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:57869200-57870200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:57869200-57870200	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
29	chr12:57869200-57870200	Flanking Bivalent TSS/Enh	NHEK	skin
30	chr12:57869200-57870400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:57869200-57870400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
32	chr12:57869200-57870400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
33	chr12:57869200-57870400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
34	chr12:57869200-57870400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
35	chr12:57869200-57870800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
36	chr12:57869200-57871400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
37	chr12:57869200-57871600	Active TSS	Right Atrium	heart
38	chr12:57869200-57874200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr12:57869200-57874800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:57869400-57870200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr12:57869400-57870200	Active TSS	Brain Angular Gyrus	brain
42	chr12:57869400-57870200	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
43	chr12:57869400-57870200	Flanking Bivalent TSS/Enh	Left Ventricle	heart
44	chr12:57869400-57870200	Flanking Active TSS	Pancreas	Pancrea
45	chr12:57869400-57870200	Transcr. at gene 5' and 3'	Spleen	Spleen
46	chr12:57869400-57870200	Flanking Bivalent TSS/Enh	HepG2	liver
47	chr12:57869400-57870200	Bivalent Enhancer	HUVEC	blood vessel
48	chr12:57869400-57870200	Flanking Bivalent TSS/Enh	NH-A	brain
49	chr12:57869400-57870400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:57869400-57870400	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood

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