Variant report

Variant	rs1398940
Chromosome Location	chr4:89937184-89937185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10004888	0.90[ASN][1000 genomes]
rs10006121	0.90[ASN][1000 genomes]
rs10009019	0.90[ASN][1000 genomes]
rs10025142	0.85[ASN][1000 genomes]
rs10028596	0.90[ASN][1000 genomes]
rs10030965	0.90[ASN][1000 genomes]
rs10033484	0.81[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10470937	0.90[ASN][1000 genomes]
rs11097206	0.88[ASN][1000 genomes]
rs11097208	0.96[ASN][1000 genomes]
rs11737016	0.89[ASN][1000 genomes]
rs11737182	0.81[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11935610	0.87[ASN][1000 genomes]
rs12512799	0.91[ASN][1000 genomes]
rs12640018	0.88[ASN][1000 genomes]
rs12645240	0.88[ASN][1000 genomes]
rs13138280	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs13148188	0.95[ASN][1000 genomes]
rs1458557	0.85[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs16996143	0.81[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs17015027	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17015052	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1708668	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1708669	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1708670	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1708681	0.96[ASN][1000 genomes]
rs1795722	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1795727	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1795729	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1795734	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795738	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1849597	1.00[ASN][1000 genomes]
rs1903006	0.89[ASN][1000 genomes]
rs1903007	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1921679	0.85[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1921683	0.91[ASN][1000 genomes]
rs1921684	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1961979	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2085601	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2090031	0.88[ASN][1000 genomes]
rs2178583	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2178584	0.85[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2178585	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2464514	0.93[ASN][1000 genomes]
rs2609275	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2670623	0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2704571	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2704573	0.81[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2704574	0.89[ASN][1000 genomes]
rs2704576	0.89[ASN][1000 genomes]
rs2704577	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2704596	0.87[ASN][1000 genomes]
rs28540701	0.90[ASN][1000 genomes]
rs28600923	0.94[ASN][1000 genomes]
rs2869969	0.85[ASN][1000 genomes]
rs2869971	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2869972	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2869973	0.91[ASN][1000 genomes]
rs28712360	0.96[ASN][1000 genomes]
rs2904261	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs34749134	0.86[ASN][1000 genomes]
rs34869341	0.88[ASN][1000 genomes]
rs35232147	0.90[ASN][1000 genomes]
rs35441198	0.92[ASN][1000 genomes]
rs4285052	0.86[ASN][1000 genomes]
rs4437212	0.84[ASN][1000 genomes]
rs4450885	0.96[ASN][1000 genomes]
rs4507326	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4642211	0.86[CHD][hapmap];0.91[JPT][hapmap]
rs4693981	0.94[ASN][1000 genomes]
rs60618725	0.81[ASN][1000 genomes]
rs62306363	0.86[ASN][1000 genomes]
rs62306364	0.86[ASN][1000 genomes]
rs62306390	0.82[ASN][1000 genomes]
rs62306391	0.81[ASN][1000 genomes]
rs6532091	0.86[ASN][1000 genomes]
rs6815703	0.90[ASN][1000 genomes]
rs6819725	0.92[ASN][1000 genomes]
rs6821678	0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs6827857	0.92[ASN][1000 genomes]
rs6834787	0.92[ASN][1000 genomes]
rs6844655	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6852373	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6852947	0.89[ASN][1000 genomes]
rs6853480	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs72877642	0.81[ASN][1000 genomes]
rs7654714	0.84[ASN][1000 genomes]
rs7656238	0.94[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs7659904	0.96[ASN][1000 genomes]
rs7660314	0.96[ASN][1000 genomes]
rs7680864	0.96[ASN][1000 genomes]
rs7686954	0.81[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7692455	0.91[ASN][1000 genomes]
rs7697075	0.81[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7697900	0.81[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7697921	0.91[ASN][1000 genomes]
rs9307053	0.88[ASN][1000 genomes]
rs9307054	0.81[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs9307055	0.81[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9307060	0.92[ASN][1000 genomes]
rs9307061	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9991237	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9991800	0.88[ASN][1000 genomes]
rs9995465	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv461577	chr4:89904124-89986326	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv594807	chr4:89904124-89986326	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89903000-89957200	Weak transcription	HSMM	muscle
2	chr4:89912200-89943800	Weak transcription	Psoas Muscle	Psoas
3	chr4:89913400-89944000	Weak transcription	Gastric	stomach
4	chr4:89921000-89950600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:89922600-89949800	Weak transcription	HMEC	breast
6	chr4:89922800-89945600	Weak transcription	A549	lung
7	chr4:89923400-89939400	Weak transcription	Primary T cells from cord blood	blood
8	chr4:89923600-89945600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:89923800-89943800	Weak transcription	Right Atrium	heart
10	chr4:89923800-89944400	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:89925600-89939400	Weak transcription	Aorta	Aorta
12	chr4:89926400-89949600	Weak transcription	Left Ventricle	heart
13	chr4:89926600-89941000	Weak transcription	Esophagus	oesophagus
14	chr4:89926800-89951400	Weak transcription	Right Ventricle	heart
15	chr4:89928400-89940000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:89928600-89937800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr4:89928600-89941600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:89928800-89939200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:89929200-89939400	Weak transcription	HSMMtube	muscle
20	chr4:89930000-89942600	Weak transcription	Brain Anterior Caudate	brain
21	chr4:89931200-89944000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:89931600-89943600	Weak transcription	Small Intestine	intestine
23	chr4:89931600-89945400	Weak transcription	Liver	Liver
24	chr4:89931800-89939400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:89932200-89943800	Weak transcription	Pancreas	Pancrea
26	chr4:89932400-89937200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:89932800-89939400	Weak transcription	NH-A	brain
28	chr4:89933600-89951400	Weak transcription	NHLF	lung
29	chr4:89933800-89941800	Weak transcription	NHDF-Ad	bronchial
30	chr4:89933800-89945400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr4:89934000-89945000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:89934200-89940200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:89934800-89938200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
34	chr4:89934800-89941200	Strong transcription	Fetal Lung	lung
35	chr4:89934800-89941800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:89935000-89937400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
37	chr4:89935200-89938000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:89935400-89939200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr4:89935800-89938400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
40	chr4:89936000-89937400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
41	chr4:89936000-89937800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
42	chr4:89936000-89938200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:89936000-89938400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
44	chr4:89936000-89938400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:89936000-89938600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:89936000-89939200	Strong transcription	Fetal Kidney	kidney
47	chr4:89936200-89937400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:89936200-89938200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:89936400-89937400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
50	chr4:89936400-89937400	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell

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