Variant report

Variant	rs10001420
Chromosome Location	chr4:89939440-89939441
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:89935095..89936816-chr4:89938623..89940372,2	K562	blood:
2	chr4:89937387..89940486-chr4:89941905..89944356,3	K562	blood:

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10019862	0.81[AMR][1000 genomes]
rs10028121	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs10033435	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10033476	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10433881	0.81[ASN][1000 genomes]
rs11734924	0.89[CEU][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1246630	0.87[ASN][1000 genomes]
rs1246633	0.87[ASN][1000 genomes]
rs1246638	0.83[ASN][1000 genomes]
rs1246641	0.83[ASN][1000 genomes]
rs12645173	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12647095	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12649875	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1272570	0.87[ASN][1000 genomes]
rs13105546	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13106968	0.87[ASN][1000 genomes]
rs13133608	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1355836	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1355837	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1379934	0.82[CHB][hapmap]
rs1398937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1398938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398943	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1458552	0.83[ASN][1000 genomes]
rs1458553	0.83[ASN][1000 genomes]
rs1458555	0.83[ASN][1000 genomes]
rs1513811	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1513812	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1513823	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1533288	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1533289	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1533294	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1708659	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1708671	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]
rs1708672	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1708673	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1708683	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1795730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1828735	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1903009	0.83[ASN][1000 genomes]
rs1996139	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2045516	0.83[ASN][1000 genomes]
rs2056013	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2102650	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2125410	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs2446295	0.87[ASN][1000 genomes]
rs2446309	0.83[ASN][1000 genomes]
rs2464511	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464521	0.87[ASN][1000 genomes]
rs2609254	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs2609263	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs2609266	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs2609274	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs2609278	0.83[ASN][1000 genomes]
rs2609281	0.83[ASN][1000 genomes]
rs2670618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2670619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2670620	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2670627	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2670628	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2704580	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2704588	0.83[ASN][1000 genomes]
rs2704591	0.83[ASN][1000 genomes]
rs2704592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2704593	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs2704602	0.83[ASN][1000 genomes]
rs2704603	0.83[ASN][1000 genomes]
rs2704606	0.83[ASN][1000 genomes]
rs28559811	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28624770	0.81[AMR][1000 genomes]
rs28658282	0.86[AMR][1000 genomes]
rs2869965	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs2869968	0.83[ASN][1000 genomes]
rs2869989	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28718401	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28869547	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2904264	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4693219	0.80[AMR][1000 genomes]
rs59698155	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6532100	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6532113	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6823241	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6826482	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6834297	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6845264	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6846010	0.81[ASN][1000 genomes]
rs7657630	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7673427	0.87[ASN][1000 genomes]
rs7697878	0.87[ASN][1000 genomes]
rs8180333	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs922027	0.83[ASN][1000 genomes]
rs9307063	0.81[ASN][1000 genomes]
rs938265	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs938267	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs973680	0.87[ASN][1000 genomes]
rs987314	0.83[ASN][1000 genomes]
rs993358	0.87[ASN][1000 genomes]
rs9999793	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999873	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:84 , 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	chr4:89926600-89941000	Weak transcription	Esophagus	oesophagus
12	chr4:89926800-89951400	Weak transcription	Right Ventricle	heart
13	chr4:89928400-89940000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:89928600-89941600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:89930000-89942600	Weak transcription	Brain Anterior Caudate	brain
16	chr4:89931200-89944000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:89931600-89943600	Weak transcription	Small Intestine	intestine
18	chr4:89931600-89945400	Weak transcription	Liver	Liver
19	chr4:89932200-89943800	Weak transcription	Pancreas	Pancrea
20	chr4:89933600-89951400	Weak transcription	NHLF	lung
21	chr4:89933800-89941800	Weak transcription	NHDF-Ad	bronchial
22	chr4:89933800-89945400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr4:89934000-89945000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:89934200-89940200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:89934800-89941200	Strong transcription	Fetal Lung	lung
26	chr4:89934800-89941800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:89936400-89939600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:89936400-89940800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:89936400-89941200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:89936400-89942200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:89936400-89943800	Weak transcription	Lung	lung
32	chr4:89936600-89941600	Weak transcription	Fetal Thymus	thymus
33	chr4:89936600-89943800	Weak transcription	Placenta	Placenta
34	chr4:89936800-89940800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:89936800-89945400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr4:89937200-89942000	Weak transcription	Fetal Heart	heart
37	chr4:89937200-89943000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr4:89937200-89944000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr4:89937200-89975600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:89937400-89939800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:89937400-89940000	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr4:89937400-89942200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:89937400-89942600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr4:89937400-89945600	Weak transcription	Osteobl	bone
45	chr4:89937800-89940400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr4:89937800-89940400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr4:89937800-89942000	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:89937800-89942000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr4:89937800-89942000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr4:89938000-89939600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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