Variant report

Variant	rs1708669
Chromosome Location	chr4:89947352-89947353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10004888	0.83[ASN][1000 genomes]
rs10006121	0.83[ASN][1000 genomes]
rs10009019	0.83[ASN][1000 genomes]
rs10028596	0.83[ASN][1000 genomes]
rs10030965	0.83[ASN][1000 genomes]
rs10033484	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10470937	0.83[ASN][1000 genomes]
rs11097206	0.81[ASN][1000 genomes]
rs11097208	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11737016	0.82[ASN][1000 genomes]
rs11737182	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11935610	0.80[ASN][1000 genomes]
rs12512799	0.84[ASN][1000 genomes]
rs12640018	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12645240	0.81[ASN][1000 genomes]
rs13138280	0.91[JPT][hapmap]
rs13148188	0.88[ASN][1000 genomes]
rs1398940	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1458557	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs16996143	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs17015027	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17015052	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1708668	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1708670	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1708681	0.94[ASN][1000 genomes]
rs1795722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795727	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1795729	0.94[ASN][1000 genomes]
rs1795734	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1795738	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1849597	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1903006	0.82[ASN][1000 genomes]
rs1903007	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1921679	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs1921683	0.84[ASN][1000 genomes]
rs1921684	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1961979	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2018779	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2085601	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2090031	0.86[ASN][1000 genomes]
rs2178583	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2178584	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2178585	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2464514	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609275	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2670623	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704571	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2704573	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2704574	0.82[ASN][1000 genomes]
rs2704576	0.82[ASN][1000 genomes]
rs2704577	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2704596	0.80[ASN][1000 genomes]
rs28540701	0.83[ASN][1000 genomes]
rs28600923	0.93[ASN][1000 genomes]
rs2869971	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2869972	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2869973	0.84[ASN][1000 genomes]
rs28712360	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2904261	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34869341	0.81[ASN][1000 genomes]
rs35232147	0.83[ASN][1000 genomes]
rs35441198	0.85[ASN][1000 genomes]
rs4285052	0.85[ASN][1000 genomes]
rs4450885	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4507326	0.83[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4642211	0.91[JPT][hapmap]
rs4693981	0.87[ASN][1000 genomes]
rs60618725	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62306363	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62306364	0.84[ASN][1000 genomes]
rs62306390	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62306391	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6815703	0.83[ASN][1000 genomes]
rs6819725	0.85[ASN][1000 genomes]
rs6821678	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs6827857	0.85[ASN][1000 genomes]
rs6834787	0.85[ASN][1000 genomes]
rs6844655	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs6852373	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6852947	0.82[ASN][1000 genomes]
rs6853480	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs72877642	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7656238	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7659904	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7660314	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7680864	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7686954	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7692455	0.83[ASN][1000 genomes]
rs7697075	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs7697900	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7697921	0.84[ASN][1000 genomes]
rs9307053	0.81[ASN][1000 genomes]
rs9307054	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs9307055	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs9307060	0.85[ASN][1000 genomes]
rs9307061	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9991237	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9991800	0.81[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:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89903000-89957200	Weak transcription	HSMM	muscle
2	chr4:89921000-89950600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:89922600-89949800	Weak transcription	HMEC	breast
4	chr4:89926400-89949600	Weak transcription	Left Ventricle	heart
5	chr4:89926800-89951400	Weak transcription	Right Ventricle	heart
6	chr4:89933600-89951400	Weak transcription	NHLF	lung
7	chr4:89937200-89975600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:89938200-89953000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:89939600-89951200	Weak transcription	NHEK	skin
10	chr4:89940200-89949800	Weak transcription	Primary T cells from cord blood	blood
11	chr4:89940200-89957800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:89940400-89956600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:89940400-89956600	Weak transcription	NH-A	brain
14	chr4:89940400-89957800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:89940400-89957800	Weak transcription	Aorta	Aorta
16	chr4:89940400-89959000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:89940400-89961000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:89940600-89954400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:89940600-89956000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:89940600-89956000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:89940600-89957800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:89940600-89957800	Weak transcription	Ovary	ovary
23	chr4:89940800-89956800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:89941200-89956000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr4:89941200-89956200	Weak transcription	Fetal Lung	lung
26	chr4:89941800-89947800	Weak transcription	Fetal Muscle Leg	muscle
27	chr4:89941800-89948000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr4:89941800-89952200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:89941800-89952400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:89941800-89952600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:89941800-89957800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:89941800-89957800	Weak transcription	Fetal Stomach	stomach
33	chr4:89942000-89947800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:89942000-89948600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:89942000-89950000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr4:89942000-89951200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr4:89942200-89949200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:89943200-89950600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr4:89944200-89951000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr4:89944200-89954000	Weak transcription	Small Intestine	intestine
41	chr4:89944200-89958000	Weak transcription	Fetal Heart	heart
42	chr4:89944200-89978000	Weak transcription	Pancreas	Pancrea
43	chr4:89944800-89948000	Weak transcription	K562	blood
44	chr4:89944800-89955400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:89945000-89948600	Weak transcription	Fetal Intestine Large	intestine
46	chr4:89945200-89948400	Weak transcription	Fetal Intestine Small	intestine
47	chr4:89945600-89947400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:89945600-89949200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr4:89945600-89957400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr4:89945600-89963000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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