Variant report

Variant	rs11939289
Chromosome Location	chr4:79433958-79433959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10023714	0.85[EUR][1000 genomes]
rs10518200	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098197	0.88[EUR][1000 genomes]
rs11098208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721380	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722061	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723383	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725388	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725573	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11727119	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11727137	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728117	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728640	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729604	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11729705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11730601	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11730636	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11730668	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731012	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731074	0.85[EUR][1000 genomes]
rs11731315	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731480	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731575	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11733290	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733471	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736504	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11932879	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11933630	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11933879	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11937000	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11937001	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11939230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11941299	0.87[EUR][1000 genomes]
rs11943426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11944743	0.82[CEU][hapmap]
rs13101600	0.88[EUR][1000 genomes]
rs1353527	0.88[EUR][1000 genomes]
rs1390742	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1484332	0.82[CEU][hapmap]
rs1496600	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1496603	0.86[EUR][1000 genomes]
rs1496604	0.87[EUR][1000 genomes]
rs17003235	1.00[ASN][1000 genomes]
rs17427362	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17429053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17429432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17429467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17429649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17429670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17429718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17429816	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17429963	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17430075	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17430137	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17430229	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17430243	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17430334	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17469341	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17469981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17470002	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17470023	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17470072	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17470303	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17470490	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17470553	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17470609	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17470811	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471069	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17471104	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17471139	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17481799	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1826845	0.87[EUR][1000 genomes]
rs28568377	0.87[EUR][1000 genomes]
rs28694126	0.88[EUR][1000 genomes]
rs34435856	0.85[EUR][1000 genomes]
rs35933858	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4416499	0.88[EUR][1000 genomes]
rs4975129	0.87[EUR][1000 genomes]
rs4975130	0.88[EUR][1000 genomes]
rs55849455	1.00[ASN][1000 genomes]
rs56681862	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56874454	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57325795	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57356999	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57558056	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57771713	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58467919	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58547899	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59347621	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59373877	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59658562	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60144489	0.87[EUR][1000 genomes]
rs60253739	0.88[EUR][1000 genomes]
rs60805155	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60991776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61185935	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61346341	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6817408	0.87[EUR][1000 genomes]
rs6819837	0.88[EUR][1000 genomes]
rs6825278	0.87[EUR][1000 genomes]
rs6827590	0.87[EUR][1000 genomes]
rs6846802	0.88[EUR][1000 genomes]
rs6850657	0.87[EUR][1000 genomes]
rs72659058	1.00[ASN][1000 genomes]
rs72873310	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72873312	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72873313	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7436657	0.88[EUR][1000 genomes]
rs7660569	0.87[EUR][1000 genomes]
rs7675866	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686157	0.87[EUR][1000 genomes]
rs931603	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931605	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931607	0.87[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	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79363400-79455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:79363800-79464200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:79378600-79455800	Weak transcription	Right Ventricle	heart
4	chr4:79385000-79467400	Weak transcription	Fetal Brain Male	brain
5	chr4:79393800-79467200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr4:79401000-79467200	Weak transcription	Psoas Muscle	Psoas
7	chr4:79403200-79449800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:79404200-79450200	Weak transcription	HMEC	breast
9	chr4:79408600-79435000	Weak transcription	Fetal Heart	heart
10	chr4:79410200-79443600	Weak transcription	HSMMtube	muscle
11	chr4:79410200-79461800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:79410800-79439800	Weak transcription	Fetal Lung	lung
13	chr4:79418000-79437800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:79420400-79445000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:79421800-79445200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:79426800-79455000	Weak transcription	Esophagus	oesophagus
17	chr4:79427600-79435200	Weak transcription	Fetal Stomach	stomach
18	chr4:79427800-79439400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:79428000-79437400	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr4:79428000-79437400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:79428000-79438400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr4:79428200-79466200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr4:79428400-79437400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:79428600-79437600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:79428600-79449800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:79428600-79459000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:79429400-79434800	Weak transcription	Fetal Kidney	kidney
28	chr4:79430200-79439800	Weak transcription	Left Ventricle	heart
29	chr4:79430200-79456000	Weak transcription	Aorta	Aorta
30	chr4:79430200-79456000	Weak transcription	Pancreas	Pancrea
31	chr4:79430600-79451400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:79430800-79435200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:79430800-79454600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:79431000-79434600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:79432200-79448600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:79432400-79435200	Enhancers	Stomach Mucosa	stomach
37	chr4:79432600-79434600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr4:79432800-79434600	Enhancers	HepG2	liver
39	chr4:79433000-79434600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:79433000-79435000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr4:79433000-79435000	Enhancers	Fetal Intestine Small	intestine
42	chr4:79433000-79435000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr4:79433000-79435200	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr4:79433000-79438200	Weak transcription	Gastric	stomach
45	chr4:79433200-79435000	Enhancers	Fetal Intestine Large	intestine
46	chr4:79433800-79434800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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