Variant report

Variant	rs9841781
Chromosome Location	chr3:157211631-157211632
allele	A/G
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	CTCF	chr3:157211580-157211730	HCM	heart:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
2	ARID3A	chr3:157211486-157211784	K562	blood:	n/a	n/a
3	CTCF	chr3:157211560-157211710	AG09319	gingival:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
4	RAD21	chr3:157211233-157211928	A549	lung:	n/a	chr3:157211607-157211626 chr3:157211617-157211624
5	CTCF	chr3:157211520-157211670	AoAF	blood vessel:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
6	CTCF	chr3:157211520-157211670	AG04450	lung:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
7	RAD21	chr3:157211363-157211853	H1-hESC	embryonic stem cell:	n/a	chr3:157211607-157211626 chr3:157211617-157211624
8	CTCF	chr3:157211560-157211710	GM12875	blood:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
9	CTCF	chr3:157211500-157211650	BE2_C	brain:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
10	CTCF	chr3:157211471-157211736	GM12878	blood:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
11	ARID3A	chr3:157211453-157211746	HepG2	liver:	n/a	n/a
12	CTCF	chr3:157211343-157212055	HCT-116	colon:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
13	CTCF	chr3:157211540-157211690	GM12868	blood:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
14	CTCF	chr3:157211580-157211730	GM12873	blood:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
15	CTCF	chr3:157211483-157211773	Hela-S3	cervix:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
16	CTCF	chr3:157211520-157211670	GM12878	blood:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
17	CTCF	chr3:157211520-157211670	GM12871	blood:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
18	RAD21	chr3:157211321-157211861	Hela-S3	cervix:	n/a	chr3:157211607-157211626 chr3:157211617-157211624
19	CTCF	chr3:157211520-157211670	GM12865	blood:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
20	CTCF	chr3:157211500-157211650	GM12875	blood:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
21	FOS	chr3:157211444-157211779	MCF10A-Er-Src	breast:	n/a	chr3:157211524-157211534 chr3:157211523-157211534 chr3:157211524-157211534 chr3:157211524-157211534 chr3:157211525-157211533 chr3:157211524-157211534
22	CTCF	chr3:157211520-157211670	WERI-Rb-1	eye:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
23	CTCF	chr3:157211560-157211710	GM12869	blood:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
24	CTCF	chr3:157211500-157211650	RPTEC	kidney:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
25	PBX3	chr3:157211243-157212079	SK-N-SH	brain:	n/a	n/a
26	CTCF	chr3:157211520-157211670	HBMEC	blood vessel:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
27	CTCF	chr3:157211540-157211690	HL-60	blood:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
28	CTCF	chr3:157211540-157211690	A549	lung:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
29	CTCF	chr3:157211535-157211712	Gliobla	brain:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
30	SMC3	chr3:157211023-157213187	SK-N-SH	brain:	n/a	chr3:157211611-157211625 chr3:157212174-157212181
31	CTCF	chr3:157211520-157211670	SAEC	small airway:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
32	CTCF	chr3:157211584-157211653	GM20000	blood:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
33	CTCF	chr3:157211500-157211650	HEEpiC	esophagus:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
34	FOXA1	chr3:157211402-157211651	A549	lung:	n/a	n/a
35	SMC3	chr3:157211306-157212068	Hela-S3	cervix:	n/a	chr3:157211611-157211625
36	CTCF	chr3:157211540-157211690	NHEK	skin:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
37	RAD21	chr3:157211456-157211727	GM12878	blood:	n/a	chr3:157211607-157211626 chr3:157211617-157211624
38	CTCF	chr3:157211560-157211710	HVMF	connective:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
39	CTCF	chr3:157211600-157211750	K562	blood:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
40	CTCF	chr3:157211520-157211670	AG10803	skin:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
41	CTCF	chr3:157211504-157211730	Pancreas_OC	pancreas:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
42	ZNF143	chr3:157211442-157211781	GM12878	blood:	n/a	n/a
43	CTCF	chr3:157211540-157211690	HA-sp	spinal cord:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
44	CTCF	chr3:157211560-157211710	NHEK	skin:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
45	CTCF	chr3:157211520-157211670	AG09319	gingival:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
46	CTCF	chr3:157211560-157211710	GM12864	blood:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
47	CTCF	chr3:157211500-157211650	GM12872	blood:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
48	CTCF	chr3:157211560-157211710	Caco-2	colon:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
49	CTCF	chr3:157211540-157211690	HMF	breast:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627
50	CTCF	chr3:157211540-157211690	GM12872	blood:	n/a	chr3:157211610-157211626 chr3:157211604-157211625 chr3:157211609-157211627

No.	Distal block	Cell Line	Cell type
1	chr3:157206521..157208283-chr3:157210267..157212147,2	K562	blood:
2	chr3:156956612..156957498-chr3:157211529..157212391,2	MCF-7	breast:
3	chr3:156922216..156922779-chr3:157211136..157211963,2	K562	blood:
4	chr3:156921924..156922726-chr3:157211041..157211777,3	MCF-7	breast:
5	chr3:157191374..157193760-chr3:157210330..157212227,2	K562	blood:
6	chr3:157211587..157213759-chr3:157215822..157218040,2	K562	blood:
7	chr3:156877680..156879425-chr3:157209675..157211718,2	MCF-7	breast:
8	chr3:157205290..157208283-chr3:157209694..157212147,2	K562	blood:

Variant related genes	Relation type
VEPH1	TF binding region
ENSG00000163660	Chromatin interaction
ENSG00000197415	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11709669	0.82[CHB][hapmap]
rs12631456	0.85[ASW][hapmap];0.94[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1378794	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1378800	0.82[CHB][hapmap]
rs1456101	0.82[CHB][hapmap]
rs1456102	0.87[CHB][hapmap]
rs17470517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1824056	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1902347	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28690487	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4679795	0.82[CHB][hapmap]
rs4679798	0.94[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4680370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs57095742	0.87[EUR][1000 genomes]
rs7639175	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9815250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9851066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9859018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9877620	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9841781	KPNA4	cis	parietal	SCAN
rs9841781	B3GALNT1	cis	cerebellum	SCAN
rs9841781	C3orf55	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157194000-157212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:157194600-157217000	Weak transcription	Pancreas	Pancrea
3	chr3:157194800-157212000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:157206600-157211800	Weak transcription	NHLF	lung
5	chr3:157210000-157212400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:157210200-157214000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:157210400-157212800	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr3:157210600-157214000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:157210600-157217000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:157210800-157211800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr3:157210800-157213800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:157211000-157211800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:157211000-157212000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:157211000-157213000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:157211000-157213200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:157211000-157216200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:157211200-157211800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:157211200-157212200	Enhancers	NHDF-Ad	bronchial
19	chr3:157211200-157213200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:157211200-157213200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr3:157211200-157213400	Enhancers	Osteobl	bone
22	chr3:157211200-157214000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:157211400-157212000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr3:157211400-157212400	Enhancers	Fetal Kidney	kidney
25	chr3:157211400-157212400	Enhancers	Fetal Lung	lung
26	chr3:157211400-157213200	Enhancers	HSMM	muscle
27	chr3:157211400-157213200	Genic enhancers	HUVEC	blood vessel
28	chr3:157211400-157213400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:157211600-157211800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr3:157211600-157212200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:157211600-157213200	Enhancers	NH-A	brain
32	chr3:157211600-157214200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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