Variant report

Variant	rs12541494
Chromosome Location	chr8:124429395-124429396
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	POLR2A	chr8:124428357-124429947	Raji	blood:	n/a	n/a
2	MYC	chr8:124428631-124429556	MCF10A-Er-Src	breast:	n/a	chr8:124429308-124429318 chr8:124428917-124428927
3	HA-E2F1	chr8:124428460-124429474	Hela-S3	cervix:	n/a	chr8:124428877-124428889 chr8:124428913-124428923 chr8:124429177-124429186 chr8:124428877-124428888
4	FOXP2	chr8:124428476-124429395	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr8:124428933-124429458	A549	lung:	n/a	n/a
6	SIN3AK20	chr8:124428660-124429500	PFSK-1	brain:	n/a	n/a
7	TCF12	chr8:124428649-124429401	ECC-1	luminal epithelium:	n/a	n/a
8	YY1	chr8:124428339-124429493	HepG2	liver:	n/a	chr8:124429180-124429194 chr8:124428916-124428930 chr8:124428758-124428772
9	SP1	chr8:124428318-124429560	A549	lung:	n/a	chr8:124428645-124428654 chr8:124428644-124428653 chr8:124429234-124429246 chr8:124428916-124428928 chr8:124428917-124428926 chr8:124428916-124428927 chr8:124428701-124428711 chr8:124429234-124429246 chr8:124428799-124428809 chr8:124428655-124428667 chr8:124428643-124428655 chr8:124428917-124428927 chr8:124428644-124428653 chr8:124428977-124428988 chr8:124428700-124428712 chr8:124428758-124428770 chr8:124428977-124428989 chr8:124428655-124428667 chr8:124428644-124428654 chr8:124428917-124428927 chr8:124428701-124428711 chr8:124428700-124428712 chr8:124428917-124428931 chr8:124428643-124428655 chr8:124428798-124428810 chr8:124428758-124428770 chr8:124429235-124429249 chr8:124428977-124428989 chr8:124428916-124428928 chr8:124428905-124428916 chr8:124428644-124428654 chr8:124428798-124428810 chr8:124428684-124428693 chr8:124429235-124429244 chr8:124428918-124428927
10	POLR2A	chr8:124428813-124429491	GM12892	blood:	n/a	n/a
11	SIN3A	chr8:124428834-124429473	GM12878	blood:	n/a	n/a
12	POLR2A	chr8:124428826-124429937	Hela-S3	cervix:	n/a	n/a
13	SIN3AK20	chr8:124428896-124429469	A549	lung:	n/a	n/a
14	RCOR1	chr8:124429296-124429590	K562	blood:	n/a	n/a
15	MAX	chr8:124428314-124429561	K562	blood:	n/a	chr8:124429308-124429318 chr8:124428917-124428927
16	POLR2A	chr8:124428883-124429480	Gliobla	brain:	n/a	n/a
17	POLR2A	chr8:124428286-124429505	HCT-116	colon:	n/a	n/a
18	POLR2A	chr8:124428326-124429942	GM18951	blood:	n/a	n/a
19	ELK1	chr8:124429379-124429414	K562	blood:	n/a	n/a
20	SIN3AK20	chr8:124428445-124429437	HepG2	liver:	n/a	n/a
21	MAX	chr8:124428290-124429628	MCF-7	breast:	n/a	chr8:124429308-124429318 chr8:124428917-124428927
22	CTCF	chr8:124429260-124429410	HA-sp	spinal cord:	n/a	n/a
23	YY1	chr8:124428917-124429446	A549	lung:	n/a	chr8:124429180-124429194
24	POLR2A	chr8:124428850-124429497	SK-N-MC	brain:	n/a	n/a
25	TAF1	chr8:124428909-124429478	K562	blood:	n/a	n/a
26	MAFK	chr8:124429153-124429689	Hela-S3	cervix:	n/a	n/a
27	MAX	chr8:124428716-124429448	K562	blood:	n/a	chr8:124429308-124429318 chr8:124428917-124428927
28	MAZ	chr8:124428340-124429718	GM12878	blood:	n/a	chr8:124429308-124429318 chr8:124428917-124428927
29	CTCF	chr8:124429260-124429410	GM06990	blood:	n/a	n/a
30	SIN3AK20	chr8:124428903-124429489	H1-hESC	embryonic stem cell:	n/a	n/a
31	HMGN3	chr8:124428428-124429879	K562	blood:	n/a	n/a
32	RCOR1	chr8:124428340-124430117	K562	blood:	n/a	n/a
33	TAF1	chr8:124428810-124429916	H1-hESC	embryonic stem cell:	n/a	n/a
34	SIN3AK20	chr8:124428332-124429570	K562	blood:	n/a	n/a
35	MYC	chr8:124428807-124429775	H1-hESC	embryonic stem cell:	n/a	chr8:124429308-124429318 chr8:124428917-124428927
36	MAX	chr8:124428212-124430255	MCF-7	breast:	n/a	chr8:124429308-124429318 chr8:124428917-124428927
37	EP300	chr8:124429033-124429517	K562	blood:	n/a	chr8:124429301-124429317
38	POLR2A	chr8:124428318-124429492	GM15510	blood:	n/a	n/a
39	JUND	chr8:124428400-124429535	K562	blood:	n/a	n/a
40	MAX	chr8:124428656-124429654	ECC-1	luminal epithelium:	n/a	chr8:124429308-124429318 chr8:124428917-124428927
41	RELA	chr8:124428929-124429887	GM15510	blood:	n/a	n/a
42	HDAC2	chr8:124428827-124429412	K562	blood:	n/a	n/a
43	SP1	chr8:124428339-124429573	H1-hESC	embryonic stem cell:	n/a	chr8:124428645-124428654 chr8:124428644-124428653 chr8:124429234-124429246 chr8:124428916-124428928 chr8:124428917-124428926 chr8:124428916-124428927 chr8:124428701-124428711 chr8:124429234-124429246 chr8:124428799-124428809 chr8:124428655-124428667 chr8:124428643-124428655 chr8:124428917-124428927 chr8:124428644-124428653 chr8:124428977-124428988 chr8:124428700-124428712 chr8:124428758-124428770 chr8:124428977-124428989 chr8:124428655-124428667 chr8:124428644-124428654 chr8:124428917-124428927 chr8:124428701-124428711 chr8:124428700-124428712 chr8:124428917-124428931 chr8:124428643-124428655 chr8:124428798-124428810 chr8:124428758-124428770 chr8:124429235-124429249 chr8:124428977-124428989 chr8:124428916-124428928 chr8:124428905-124428916 chr8:124428644-124428654 chr8:124428798-124428810 chr8:124428684-124428693 chr8:124429235-124429244 chr8:124428918-124428927
44	TBL1XR1	chr8:124428907-124429490	K562	blood:	n/a	n/a
45	CTCF	chr8:124429320-124429470	GM12870	blood:	n/a	n/a
46	CCNT2	chr8:124428344-124429402	K562	blood:	n/a	chr8:124428645-124428654
47	CTCF	chr8:124429102-124429455	GM12878	blood:	n/a	n/a
48	EGR1	chr8:124428448-124429482	K562	blood:	n/a	chr8:124428972-124428982 chr8:124428918-124428928 chr8:124428979-124428994 chr8:124429181-124429190 chr8:124428801-124428814 chr8:124428980-124428993 chr8:124428917-124428927
49	MAX	chr8:124428354-124429558	SK-N-SH	brain:	n/a	chr8:124429308-124429318 chr8:124428917-124428927
50	NFIC	chr8:124428835-124429577	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:124283829..124288838-chr8:124426117..124430573,9	K562	blood:
2	chr8:124285038..124289042-chr8:124427512..124430569,10	MCF-7	breast:
3	chr8:124283849..124288367-chr8:124426037..124430184,7	K562	blood:
4	chr10:102820879..102821499-chr8:124429095..124429824,2	Hela-S3	cervix:
5	chr8:124411247..124413629-chr8:124428301..124430441,2	K562	blood:
6	chr8:124406056..124410111-chr8:124427174..124433258,8	MCF-7	breast:
7	chr8:124253290..124255259-chr8:124427452..124430915,4	MCF-7	breast:
8	chr8:124287117..124289356-chr8:124428879..124431490,3	MCF-7	breast:
9	chr8:124406688..124410730-chr8:124426992..124430866,9	K562	blood:
10	chr8:124404505..124411576-chr8:124423647..124430734,19	MCF-7	breast:
11	chr8:124428663..124430757-chr8:124778757..124780951,2	K562	blood:
12	chr8:124405499..124410730-chr8:124426606..124431705,19	K562	blood:
13	chr11:62623530..62624100-chr8:124428998..124429986,2	Hela-S3	cervix:
14	chr8:124427319..124431344-chr8:124440107..124444172,5	MCF-7	breast:
15	chr1:108743710..108745219-chr8:124429078..124431227,2	MCF-7	breast:
16	chr8:124427993..124430634-chr8:124780278..124783215,3	MCF-7	breast:

Variant related genes	Relation type
ATAD2	TF binding region
ENSG00000156795	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000189376	Chromatin interaction
ENSG00000156802	Chromatin interaction
ENSG00000176853	Chromatin interaction
ENSG00000165156	Chromatin interaction
ENSG00000254294	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10091979	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10106648	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10106777	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10110934	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10447969	0.81[JPT][hapmap]
rs1045270	0.81[JPT][hapmap]
rs1045284	0.81[JPT][hapmap]
rs1045291	0.81[JPT][hapmap]
rs10505436	0.81[JPT][hapmap]
rs10505437	0.81[JPT][hapmap]
rs11780128	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11786724	0.81[JPT][hapmap]
rs11989576	0.81[JPT][hapmap]
rs11991520	0.81[JPT][hapmap]
rs12235062	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12541769	0.80[CHD][hapmap]
rs12545841	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12547262	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12675771	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13265652	0.83[JPT][hapmap]
rs13265801	0.81[JPT][hapmap]
rs13269287	0.81[JPT][hapmap]
rs13272492	0.81[JPT][hapmap]
rs13278697	0.81[JPT][hapmap]
rs13278992	0.81[JPT][hapmap]
rs1967032	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28485832	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28570131	0.88[EUR][1000 genomes]
rs28633322	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3765211	0.81[JPT][hapmap]
rs3765212	0.81[JPT][hapmap]
rs3779984	0.81[JPT][hapmap]
rs3779986	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3817716	0.81[JPT][hapmap]
rs3824250	0.81[JPT][hapmap]
rs3824253	0.81[JPT][hapmap]
rs3824254	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3824255	0.81[JPT][hapmap]
rs3905739	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3955451	0.81[JPT][hapmap]
rs4870853	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4871363	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4871378	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4871380	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55766597	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57128794	0.81[EUR][1000 genomes]
rs6415480	0.81[JPT][hapmap]
rs6470147	0.81[JPT][hapmap]
rs6470153	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6982267	0.81[JPT][hapmap]
rs6993896	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6994481	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6999234	0.81[JPT][hapmap]
rs7001767	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7012822	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7014678	0.81[JPT][hapmap]
rs7341643	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7822061	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs7825449	0.81[JPT][hapmap]
rs7825955	0.81[JPT][hapmap]
rs7827492	0.91[CHB][hapmap];0.90[JPT][hapmap]

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	nsv831449	chr8:124276685-124471740	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3415547	chr8:124420820-124444289	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12541494	FLJ10204	cis	multi-tissue	Pritchard
rs12541494	WDYHV1	cis	lung	GTEx
rs12541494	WDYHV1	cis	Heart Left Ventricle	GTEx
rs12541494	WDYHV1	cis	lymphoblastoid	seeQTL
rs12541494	WDYHV1	cis	cerebellum	SCAN
rs12541494	TATDN1	cis	cerebellum	SCAN
rs12541494	WDYHV1	cis	Muscle Skeletal	GTEx
rs12541494	C8orf32	cis	multi-tissue	Pritchard
rs12541494	WDYHV1	cis	Lymphoblastoid	GTEx
rs12541494	ATAD2	cis	cerebellum	SCAN
rs12541494	C8orf32	cis	normal skin	skin_eQTL
rs12541494	WDYHV1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:124427600-124430200	Active TSS	A549	lung
2	chr8:124427800-124429600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr8:124427800-124429600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr8:124427800-124429600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr8:124427800-124429600	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr8:124427800-124429600	Active TSS	Pancreas	Pancrea
7	chr8:124427800-124429800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr8:124427800-124429800	Active TSS	Right Ventricle	heart
9	chr8:124428000-124429400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr8:124428000-124429400	Active TSS	Monocytes-CD14+_RO01746	blood
11	chr8:124428000-124429600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:124428000-124429600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr8:124428000-124429600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr8:124428000-124429600	Active TSS	Brain Angular Gyrus	brain
15	chr8:124428000-124429600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr8:124428000-124429600	Active TSS	Fetal Brain Female	brain
17	chr8:124428000-124429600	Active TSS	Gastric	stomach
18	chr8:124428000-124429600	Active TSS	Left Ventricle	heart
19	chr8:124428000-124429600	Active TSS	Rectal Smooth Muscle	rectum
20	chr8:124428000-124429600	Active TSS	Stomach Smooth Muscle	stomach
21	chr8:124428000-124429600	Active TSS	HMEC	breast
22	chr8:124428000-124429600	Active TSS	HSMM	muscle
23	chr8:124428000-124430000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr8:124428000-124430000	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr8:124428200-124429400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr8:124428200-124429400	Active TSS	Placenta	Placenta
27	chr8:124428200-124429400	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr8:124428200-124429600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr8:124428200-124429600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr8:124428200-124429600	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr8:124428200-124429600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr8:124428200-124429600	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr8:124428200-124429600	Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr8:124428200-124429600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr8:124428200-124429600	Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr8:124428200-124429600	Active TSS	Brain Anterior Caudate	brain
37	chr8:124428200-124429600	Active TSS	Brain Cingulate Gyrus	brain
38	chr8:124428200-124429600	Active TSS	Brain Germinal Matrix	brain
39	chr8:124428200-124429600	Active TSS	Brain Hippocampus Middle	brain
40	chr8:124428200-124429600	Active TSS	Brain Substantia Nigra	brain
41	chr8:124428200-124429600	Active TSS	Colonic Mucosa	Colon
42	chr8:124428200-124429600	Active TSS	Duodenum Mucosa	Duodenum
43	chr8:124428200-124429600	Active TSS	Esophagus	oesophagus
44	chr8:124428200-124429600	Active TSS	Fetal Heart	heart
45	chr8:124428200-124429600	Active TSS	Fetal Lung	lung
46	chr8:124428200-124429600	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr8:124428200-124429600	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr8:124428200-124429600	Active TSS	Small Intestine	intestine
49	chr8:124428200-124429600	Active TSS	Thymus	Thymus
50	chr8:124428200-124429600	Active TSS	HSMMtube	muscle

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