Variant report

Variant	rs12508661
Chromosome Location	chr4:74451092-74451093
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:74448932..74451410-chr4:74453636..74455838,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10011419	0.87[EUR][1000 genomes]
rs10019146	0.89[CEU][hapmap];0.91[JPT][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs10019320	0.87[EUR][1000 genomes]
rs10020054	0.87[EUR][1000 genomes]
rs10021827	0.87[EUR][1000 genomes]
rs10029673	0.94[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10518115	1.00[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs1074085	0.89[EUR][1000 genomes]
rs1247651	0.84[EUR][1000 genomes]
rs1247668	0.90[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs1247670	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs1247671	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs12503916	0.90[CEU][hapmap];0.91[JPT][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs12505842	0.87[EUR][1000 genomes]
rs12506668	0.87[EUR][1000 genomes]
rs12506675	0.87[EUR][1000 genomes]
rs12507775	0.90[CEU][hapmap];0.91[JPT][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs13133747	0.97[EUR][1000 genomes]
rs13144296	0.89[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs13144390	0.89[EUR][1000 genomes]
rs1358592	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs1528915	0.86[EUR][1000 genomes]
rs1528916	0.80[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs1528917	0.90[CEU][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs1528918	0.86[CEU][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs1569204	0.90[CEU][hapmap]
rs16849628	0.90[CEU][hapmap];0.91[JPT][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs16849629	0.87[EUR][1000 genomes]
rs16849651	0.87[EUR][1000 genomes]
rs16849656	0.87[EUR][1000 genomes]
rs16849659	0.87[EUR][1000 genomes]
rs16849675	0.88[EUR][1000 genomes]
rs16849677	0.90[CEU][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs16849727	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs17192413	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17805623	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008288	0.90[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs2204736	0.86[EUR][1000 genomes]
rs28407399	0.87[EUR][1000 genomes]
rs28450939	0.87[EUR][1000 genomes]
rs28612539	0.87[EUR][1000 genomes]
rs28658027	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28693538	0.87[EUR][1000 genomes]
rs34123018	0.98[EUR][1000 genomes]
rs34773614	0.88[EUR][1000 genomes]
rs34832471	0.86[EUR][1000 genomes]
rs34859660	0.88[EUR][1000 genomes]
rs35988516	0.85[EUR][1000 genomes]
rs3756073	0.83[EUR][1000 genomes]
rs4694170	0.85[CEU][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs4694626	0.89[EUR][1000 genomes]
rs68145475	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6838329	0.91[EUR][1000 genomes]
rs72649103	0.92[EUR][1000 genomes]
rs7665563	0.88[EUR][1000 genomes]
rs7665972	0.88[EUR][1000 genomes]
rs7667019	0.88[EUR][1000 genomes]
rs7667185	0.88[EUR][1000 genomes]
rs7674913	0.87[EUR][1000 genomes]
rs7676850	0.87[EUR][1000 genomes]
rs7676870	0.87[EUR][1000 genomes]
rs7676884	0.87[EUR][1000 genomes]
rs7682201	0.90[CEU][hapmap];0.91[JPT][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs7687216	0.83[EUR][1000 genomes]
rs7695792	0.88[EUR][1000 genomes]
rs7695946	0.88[EUR][1000 genomes]
rs7696502	0.87[EUR][1000 genomes]
rs9999939	0.90[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv1792624	chr4:74437054-74453857	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12508661	MUC7	cis	cerebellum	SCAN
rs12508661	ART3	cis	cerebellum	SCAN
rs12508661	CCNG2	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74438000-74464800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:74440200-74451200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:74440200-74455200	Weak transcription	Fetal Intestine Small	intestine
4	chr4:74440200-74457400	Weak transcription	Pancreas	Pancrea
5	chr4:74440200-74472600	Weak transcription	Gastric	stomach
6	chr4:74441200-74464800	Weak transcription	Placenta	Placenta
7	chr4:74443600-74455400	Weak transcription	Stomach Mucosa	stomach
8	chr4:74446200-74456000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr4:74447000-74456000	Strong transcription	Fetal Thymus	thymus
10	chr4:74447600-74455000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:74447600-74463400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr4:74448600-74451200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr4:74448800-74456000	Weak transcription	Fetal Intestine Large	intestine
14	chr4:74449000-74451200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:74449000-74470200	Weak transcription	Primary T cells from cord blood	blood
16	chr4:74449400-74451200	Strong transcription	Thymus	Thymus
17	chr4:74449800-74451200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr4:74449800-74451200	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr4:74449800-74454800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:74449800-74455200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr4:74449800-74461600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:74450200-74453400	Enhancers	Muscle Satellite Cultured Cells	--
23	chr4:74450200-74455200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:74450600-74451200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:74450600-74451400	Weak transcription	NHEK	skin
26	chr4:74450600-74455000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr4:74450800-74451200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:74450800-74454800	Weak transcription	HMEC	breast
29	chr4:74451000-74451200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:74451000-74452800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:74451000-74455400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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