Variant report

Variant	rs1961979
Chromosome Location	chr4:89922437-89922438
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:89917204..89919700-chr4:89921464..89923708,2	K562	blood:
2	chr4:89918481..89920513-chr4:89921696..89923583,2	MCF-7	breast:
3	chr4:89916625..89919056-chr4:89920360..89922873,2	MCF-7	breast:
4	chr4:89920516..89923501-chr4:89978516..89980046,2	K562	blood:

Extended variants
information (count: 116 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10004888	0.93[ASN][1000 genomes]
rs10006121	0.93[ASN][1000 genomes]
rs10009019	0.93[ASN][1000 genomes]
rs10025142	0.88[ASN][1000 genomes]
rs10028596	0.93[ASN][1000 genomes]
rs10030965	0.93[ASN][1000 genomes]
rs10033484	0.80[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10470937	0.93[ASN][1000 genomes]
rs11097206	0.91[ASN][1000 genomes]
rs11097208	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11732617	0.82[ASN][1000 genomes]
rs11737016	0.93[ASN][1000 genomes]
rs11737182	0.80[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11935610	0.91[ASN][1000 genomes]
rs12512799	0.95[ASN][1000 genomes]
rs12640018	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12645240	0.91[ASN][1000 genomes]
rs13138280	0.86[JPT][hapmap]
rs13148188	0.99[ASN][1000 genomes]
rs1398940	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1458557	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16996143	0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17015027	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes]
rs17015052	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1708668	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1708669	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]
rs1708670	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1708681	0.92[ASN][1000 genomes]
rs1795722	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1795727	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1795729	0.95[ASN][1000 genomes]
rs1795734	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1795738	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1849597	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1903006	0.93[ASN][1000 genomes]
rs1903007	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1921679	0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1921683	0.95[ASN][1000 genomes]
rs1921684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2085601	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2090031	0.84[ASN][1000 genomes]
rs2178583	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2178584	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2178585	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2464514	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2609275	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2609277	0.82[ASN][1000 genomes]
rs2670623	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2704571	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2704573	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2704574	0.93[ASN][1000 genomes]
rs2704576	0.93[ASN][1000 genomes]
rs2704577	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2704596	0.91[ASN][1000 genomes]
rs28540701	0.93[ASN][1000 genomes]
rs28600923	0.91[ASN][1000 genomes]
rs2869969	0.88[ASN][1000 genomes]
rs2869971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869973	0.95[ASN][1000 genomes]
rs28712360	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2904261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34749134	0.90[ASN][1000 genomes]
rs34869341	0.92[ASN][1000 genomes]
rs35232147	0.93[ASN][1000 genomes]
rs35441198	0.96[ASN][1000 genomes]
rs4285052	0.83[ASN][1000 genomes]
rs4437212	0.87[ASN][1000 genomes]
rs4450885	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4507326	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4642211	0.86[JPT][hapmap]
rs4693981	0.98[ASN][1000 genomes]
rs60618725	0.83[AMR][1000 genomes]
rs62306363	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62306364	0.82[ASN][1000 genomes]
rs62306390	0.84[AMR][1000 genomes]
rs62306391	0.83[AMR][1000 genomes]
rs6532091	0.90[ASN][1000 genomes]
rs67308941	0.81[ASN][1000 genomes]
rs6815703	0.93[ASN][1000 genomes]
rs6819725	0.96[ASN][1000 genomes]
rs6821678	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs6827857	0.96[ASN][1000 genomes]
rs6834787	0.96[ASN][1000 genomes]
rs6844655	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6852373	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6852947	0.93[ASN][1000 genomes]
rs6853480	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs72877642	0.83[AMR][1000 genomes]
rs7654714	0.87[ASN][1000 genomes]
rs7656238	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7659904	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7660314	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7660385	0.81[ASN][1000 genomes]
rs7680864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7686954	0.80[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7692455	0.94[ASN][1000 genomes]
rs7697075	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7697900	0.80[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7697921	0.95[ASN][1000 genomes]
rs9307053	0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs9307054	0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9307055	0.81[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs9307060	0.96[ASN][1000 genomes]
rs9307061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9991237	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9991800	0.91[ASN][1000 genomes]
rs9995465	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv998651	chr4:89800245-89933445	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv537175	chr4:89800245-89933445	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89878400-89927600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:89896800-89934800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr4:89903000-89957200	Weak transcription	HSMM	muscle
4	chr4:89903400-89936000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:89904200-89927600	Weak transcription	Pancreas	Pancrea
6	chr4:89906600-89927400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:89907800-89927400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:89908400-89926600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:89908800-89927400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr4:89909400-89926400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:89909800-89931200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:89910400-89927600	Weak transcription	Ovary	ovary
13	chr4:89910800-89923400	Weak transcription	Fetal Stomach	stomach
14	chr4:89911400-89930400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr4:89911600-89926400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:89911600-89926600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:89912200-89926200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:89912200-89926400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:89912200-89935800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr4:89912200-89943800	Weak transcription	Psoas Muscle	Psoas
21	chr4:89912400-89923200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:89912400-89927600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:89913400-89923400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr4:89913400-89930800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr4:89913400-89944000	Weak transcription	Gastric	stomach
26	chr4:89913600-89923200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:89915800-89927200	Weak transcription	Fetal Muscle Leg	muscle
28	chr4:89916200-89923400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:89917200-89927400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:89918200-89923400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr4:89918200-89923800	Enhancers	Fetal Intestine Large	intestine
32	chr4:89918600-89923800	Enhancers	Fetal Intestine Small	intestine
33	chr4:89919400-89926600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr4:89920000-89927200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr4:89920200-89923800	Enhancers	Duodenum Mucosa	Duodenum
36	chr4:89920400-89937000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr4:89921000-89930000	Weak transcription	Liver	Liver
38	chr4:89921000-89950600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr4:89921400-89922800	Enhancers	Hela-S3	cervix
40	chr4:89921400-89923800	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr4:89921600-89922600	Genic enhancers	K562	blood
42	chr4:89921600-89922800	Enhancers	HepG2	liver
43	chr4:89921600-89923800	Enhancers	Colon Smooth Muscle	Colon
44	chr4:89921600-89924800	Enhancers	Fetal Brain Male	brain
45	chr4:89921800-89922800	Enhancers	A549	lung
46	chr4:89921800-89922800	Enhancers	HUVEC	blood vessel
47	chr4:89921800-89925000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:89922000-89922600	Enhancers	Placenta	Placenta
49	chr4:89922000-89922800	Enhancers	NHEK	skin
50	chr4:89922000-89923000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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