Variant report

Variant	rs1708671
Chromosome Location	chr4:89943154-89943155
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:89937387..89940486-chr4:89941905..89944356,3	K562	blood:
2	chr4:89441809..89444067-chr4:89942046..89944719,2	K562	blood:
3	chr4:89942555..89945377-chr4:89950221..89952827,2	K562	blood:

Variant related genes	Relation type
ENSG00000138640	Chromatin interaction
ENSG00000138641	Chromatin interaction
ENSG00000255072	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10001420	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10028121	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10033435	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10033476	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10433881	0.85[ASN][1000 genomes]
rs11734924	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1246630	0.84[ASN][1000 genomes]
rs1246633	0.84[ASN][1000 genomes]
rs12645173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12647095	0.85[ASN][1000 genomes]
rs12649875	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1272570	0.84[ASN][1000 genomes]
rs13105546	0.85[ASN][1000 genomes]
rs13106968	0.84[ASN][1000 genomes]
rs13133608	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13138927	0.81[ASN][1000 genomes]
rs1355836	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1355837	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1379934	0.82[CHB][hapmap]
rs1398937	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1398938	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1398939	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1398941	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1398943	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1513811	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1513812	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1513823	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1533288	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1533289	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1533294	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1708659	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1708672	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1708673	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1708683	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795730	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795735	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795737	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795740	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1828735	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1996139	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2056013	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2102650	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2125410	0.82[CHB][hapmap]
rs2446295	0.84[ASN][1000 genomes]
rs2464511	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2464521	0.84[ASN][1000 genomes]
rs2609254	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs2609263	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs2609266	0.92[CEU][hapmap]
rs2609274	0.82[CHB][hapmap]
rs2670618	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2670619	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2670620	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2670627	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2670628	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704585	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704592	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704593	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs28559811	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28658282	0.81[AMR][1000 genomes]
rs2869965	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs2869989	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28718401	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28869547	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2904264	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4325981	0.81[ASN][1000 genomes]
rs4693219	0.85[AMR][1000 genomes]
rs4693984	0.83[AMR][1000 genomes]
rs4693987	0.81[ASN][1000 genomes]
rs59698155	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6532100	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6532113	0.85[ASN][1000 genomes]
rs6823241	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6826482	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6834297	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6845264	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6846010	0.85[ASN][1000 genomes]
rs7657630	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7673427	0.84[ASN][1000 genomes]
rs7697878	0.84[ASN][1000 genomes]
rs8180333	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9307063	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs938265	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs938267	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs973680	0.84[ASN][1000 genomes]
rs993358	0.84[ASN][1000 genomes]
rs9999793	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9999873	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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:80 , 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	chr4:89923600-89945600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:89923800-89943800	Weak transcription	Right Atrium	heart
9	chr4:89923800-89944400	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:89926400-89949600	Weak transcription	Left Ventricle	heart
11	chr4:89926800-89951400	Weak transcription	Right Ventricle	heart
12	chr4:89931200-89944000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:89931600-89943600	Weak transcription	Small Intestine	intestine
14	chr4:89931600-89945400	Weak transcription	Liver	Liver
15	chr4:89932200-89943800	Weak transcription	Pancreas	Pancrea
16	chr4:89933600-89951400	Weak transcription	NHLF	lung
17	chr4:89933800-89945400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr4:89934000-89945000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:89936400-89943800	Weak transcription	Lung	lung
20	chr4:89936600-89943800	Weak transcription	Placenta	Placenta
21	chr4:89936800-89945400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr4:89937200-89944000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr4:89937200-89975600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:89937400-89945600	Weak transcription	Osteobl	bone
25	chr4:89938200-89943200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr4:89938200-89943200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:89938200-89944400	Weak transcription	Adipose Nuclei	Adipose
28	chr4:89938200-89953000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:89939600-89951200	Weak transcription	NHEK	skin
30	chr4:89940000-89945200	Weak transcription	Fetal Kidney	kidney
31	chr4:89940200-89943400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:89940200-89945000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:89940200-89949800	Weak transcription	Primary T cells from cord blood	blood
34	chr4:89940200-89957800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:89940400-89943600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:89940400-89944000	Weak transcription	HSMMtube	muscle
37	chr4:89940400-89944600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:89940400-89944800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr4:89940400-89956600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:89940400-89956600	Weak transcription	NH-A	brain
41	chr4:89940400-89957800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:89940400-89957800	Weak transcription	Aorta	Aorta
43	chr4:89940400-89959000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:89940400-89961000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr4:89940600-89943800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:89940600-89954400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:89940600-89956000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:89940600-89956000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr4:89940600-89957800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr4:89940600-89957800	Weak transcription	Ovary	ovary

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