Variant report

Variant	rs12501990
Chromosome Location	chr4:57805166-57805167
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57803794..57806206-chr4:57808007..57809597,2	K562	blood:

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10008356	0.83[ASN][1000 genomes]
rs10030913	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10866440	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10866441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1105434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107675	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11729152	0.82[ASN][1000 genomes]
rs11730321	0.94[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs11730476	0.81[ASN][1000 genomes]
rs11730525	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11734953	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11736192	0.82[ASN][1000 genomes]
rs11736808	0.86[ASN][1000 genomes]
rs11736869	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11736965	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11737689	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11932673	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11933908	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12500454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12501224	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12502076	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12641030	0.81[AMR][1000 genomes]
rs1277287	1.00[JPT][hapmap]
rs13108245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13113802	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13116564	0.87[ASN][1000 genomes]
rs13119525	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13123018	0.86[EUR][1000 genomes]
rs13131605	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13136432	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13146539	0.80[ASN][1000 genomes]
rs13146960	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13149162	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13150593	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13152476	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13353552	0.87[ASN][1000 genomes]
rs1625691	1.00[JPT][hapmap]
rs17081937	1.00[JPT][hapmap]
rs17087307	0.80[ASN][1000 genomes]
rs17087317	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17087411	0.87[JPT][hapmap]
rs17087414	0.87[JPT][hapmap]
rs1718839	1.00[JPT][hapmap]
rs1877669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1963666	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1976780	0.80[ASN][1000 genomes]
rs2002153	0.84[ASN][1000 genomes]
rs2014870	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2090962	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2228991	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2412772	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs3000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34124552	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34448457	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34659774	0.80[ASN][1000 genomes]
rs35267092	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3733306	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs3796528	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3806745	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4276341	0.87[ASN][1000 genomes]
rs4339274	0.82[CEU][hapmap]
rs4864606	0.90[ASN][1000 genomes]
rs4864607	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4864608	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4865156	0.81[ASN][1000 genomes]
rs4865157	0.83[ASN][1000 genomes]
rs4865158	0.82[ASN][1000 genomes]
rs4865159	0.84[ASN][1000 genomes]
rs4865160	0.84[ASN][1000 genomes]
rs4865172	0.88[CEU][hapmap]
rs55822707	0.88[ASN][1000 genomes]
rs56122758	0.81[ASN][1000 genomes]
rs62308110	0.81[ASN][1000 genomes]
rs62308111	0.81[ASN][1000 genomes]
rs62308135	0.90[ASN][1000 genomes]
rs62308136	0.90[ASN][1000 genomes]
rs62308137	0.89[ASN][1000 genomes]
rs62308155	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6554393	0.83[ASN][1000 genomes]
rs6554394	0.83[ASN][1000 genomes]
rs6554397	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6554398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6554399	0.89[ASN][1000 genomes]
rs6816950	0.81[ASN][1000 genomes]
rs6838948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6840805	0.81[ASN][1000 genomes]
rs6847086	0.82[JPT][hapmap]
rs6852110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6854420	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6855212	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6858216	0.81[ASN][1000 genomes]
rs729844	0.87[ASN][1000 genomes]
rs73242609	0.90[ASN][1000 genomes]
rs73242616	0.87[ASN][1000 genomes]
rs7661194	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7666804	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7667302	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7680140	0.82[CEU][hapmap]
rs7680734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7685576	0.87[ASN][1000 genomes]
rs7695970	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs781666	1.00[JPT][hapmap]
rs781668	1.00[JPT][hapmap]
rs781669	0.85[ASN][1000 genomes]
rs899632	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9684742	0.87[ASN][1000 genomes]
rs9685436	0.82[CEU][hapmap]
rs9942208	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv3425352	chr4:57783591-57820951	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12501990	RP11-738E22.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57777600-57805600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:57777600-57806000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:57780800-57808200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:57793600-57842000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:57793600-57842000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:57797600-57805400	Weak transcription	Brain Germinal Matrix	brain
7	chr4:57797600-57805400	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:57797600-57807000	Weak transcription	Gastric	stomach
9	chr4:57797600-57811800	Weak transcription	Stomach Mucosa	stomach
10	chr4:57798000-57805800	Weak transcription	Fetal Brain Female	brain
11	chr4:57798000-57806000	Weak transcription	Brain Substantia Nigra	brain
12	chr4:57798000-57806400	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:57798000-57809400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr4:57798000-57814200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr4:57798200-57805600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:57798200-57805600	Weak transcription	Brain Anterior Caudate	brain
17	chr4:57798200-57809600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr4:57798200-57811800	Weak transcription	Esophagus	oesophagus
19	chr4:57798200-57828400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr4:57798200-57829600	Weak transcription	Pancreas	Pancrea
21	chr4:57798400-57805800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:57798400-57806000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr4:57798400-57806400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:57798400-57808200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:57798400-57810800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr4:57798400-57811800	Weak transcription	Fetal Kidney	kidney
27	chr4:57798400-57814000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:57798400-57828200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr4:57798600-57828200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr4:57799400-57808600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:57799800-57805800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr4:57799800-57807400	Weak transcription	Small Intestine	intestine
33	chr4:57799800-57809000	Weak transcription	HepG2	liver
34	chr4:57800000-57805600	Weak transcription	GM12878-XiMat	blood
35	chr4:57800000-57807200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:57800200-57811000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr4:57800400-57805600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:57800400-57809400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr4:57801600-57806000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:57801800-57808600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:57802000-57805400	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr4:57802200-57806000	Strong transcription	Fetal Intestine Small	intestine
43	chr4:57802200-57807000	Strong transcription	Fetal Stomach	stomach
44	chr4:57802400-57806000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr4:57802400-57806000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:57802400-57806800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:57802600-57805400	Strong transcription	Adipose Nuclei	Adipose
48	chr4:57802600-57805800	Strong transcription	Placenta	Placenta
49	chr4:57802600-57806000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:57802600-57806000	Strong transcription	HUES6 Cell Line	embryonic stem cell

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