Variant report

Variant	rs2083486
Chromosome Location	chr1:47169210-47169211
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47166194..47168909-chr1:47169086..47171006,2	MCF-7	breast:
2	chr1:47150911..47153392-chr1:47166630..47169544,2	K562	blood:
3	chr1:47167694..47169718-chr1:47177678..47180403,2	MCF-7	breast:
4	chr1:47150911..47153746-chr1:47167363..47169544,2	K562	blood:
5	chr1:47169118..47170712-chr1:47210648..47212362,2	K562	blood:

Variant related genes	Relation type
ENSG00000159658	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10158678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10159351	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1025806	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs1048351	0.97[EUR][1000 genomes]
rs1048380	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs1075982	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs10890411	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10890412	0.86[JPT][hapmap]
rs10890416	0.81[EUR][1000 genomes]
rs11211334	0.85[JPT][hapmap]
rs11211338	0.97[EUR][1000 genomes]
rs11211340	0.87[JPT][hapmap]
rs11211341	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211344	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211346	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1139758	0.94[EUR][1000 genomes]
rs1150064	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150068	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11801316	0.96[EUR][1000 genomes]
rs11801419	0.91[EUR][1000 genomes]
rs11804665	0.94[EUR][1000 genomes]
rs12047537	0.94[EUR][1000 genomes]
rs12048954	0.85[JPT][hapmap]
rs12078635	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12082387	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12094663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1258000	0.84[EUR][1000 genomes]
rs1258002	0.83[EUR][1000 genomes]
rs1258052	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1258053	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1258054	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1258056	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1258059	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1440485	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap]
rs1440486	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs1440489	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1440490	0.84[CEU][hapmap]
rs17102352	0.94[EUR][1000 genomes]
rs17102355	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs17102428	0.94[CEU][hapmap]
rs17102473	0.94[EUR][1000 genomes]
rs1745377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1933933	0.94[EUR][1000 genomes]
rs1962900	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1971519	0.89[CEU][hapmap]
rs2119301	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs2218189	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2241862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2275380	0.85[JPT][hapmap]
rs2289446	0.94[EUR][1000 genomes]
rs2289447	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs2304745	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs2405026	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs2405030	1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34932727	0.97[EUR][1000 genomes]
rs3737731	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs3766211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766214	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3766215	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs3766217	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs3766219	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3766224	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4272563	1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4274009	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs4301586	0.96[EUR][1000 genomes]
rs4443838	0.94[EUR][1000 genomes]
rs55914029	0.95[EUR][1000 genomes]
rs56319728	0.83[EUR][1000 genomes]
rs58185502	0.92[EUR][1000 genomes]
rs585257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs594118	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs595813	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59881815	0.94[EUR][1000 genomes]
rs60173509	0.94[EUR][1000 genomes]
rs60675294	0.98[EUR][1000 genomes]
rs611468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs614486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61782563	0.97[EUR][1000 genomes]
rs61782564	0.97[EUR][1000 genomes]
rs61782568	0.98[EUR][1000 genomes]
rs61782590	0.85[EUR][1000 genomes]
rs61784001	0.94[EUR][1000 genomes]
rs61784002	0.94[EUR][1000 genomes]
rs61784003	0.97[EUR][1000 genomes]
rs618554	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs618878	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs620431	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs620913	0.88[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs625507	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs625590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs637760	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs638845	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6429607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6429608	0.91[EUR][1000 genomes]
rs6429609	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs647999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6666405	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6667885	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669393	0.94[EUR][1000 genomes]
rs6670495	0.89[CEU][hapmap]
rs6671005	0.97[EUR][1000 genomes]
rs6671124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688195	0.98[EUR][1000 genomes]
rs723334	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs723690	0.89[CEU][hapmap]
rs732539	0.97[EUR][1000 genomes]
rs7354865	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs7354894	0.89[CEU][hapmap]
rs7412469	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs744096	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs7519866	0.91[EUR][1000 genomes]
rs7532601	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7541868	0.97[EUR][1000 genomes]
rs7553243	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8851	0.86[EUR][1000 genomes]
rs946320	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2083486	KIAA0494	Cis_1M	lymphoblastoid	RTeQTL
rs2083486	ATPAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47141400-47183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:47143800-47171600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:47154600-47183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:47157600-47172200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:47158200-47172000	Weak transcription	Brain Angular Gyrus	brain
6	chr1:47158800-47171000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:47159200-47182800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:47159400-47171200	Weak transcription	Right Ventricle	heart
9	chr1:47159400-47172200	Weak transcription	Psoas Muscle	Psoas
10	chr1:47160600-47169400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:47160600-47173600	Strong transcription	Primary T cells from cord blood	blood
12	chr1:47160600-47174000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:47160600-47181200	Strong transcription	Dnd41	blood
14	chr1:47160800-47174000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:47160800-47175400	Strong transcription	Liver	Liver
16	chr1:47160800-47181800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:47160800-47182200	Strong transcription	Primary B cells from cord blood	blood
18	chr1:47160800-47182200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:47160800-47182400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:47160800-47182600	Strong transcription	Placenta	Placenta
21	chr1:47161000-47173400	Strong transcription	Primary hematopoietic stem cells	blood
22	chr1:47161000-47173800	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:47161200-47182200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr1:47161400-47182200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:47161400-47182800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:47161600-47170800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:47161800-47169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:47161800-47170600	Weak transcription	Fetal Intestine Small	intestine
29	chr1:47162000-47169800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr1:47162200-47170000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:47162200-47170200	Weak transcription	Small Intestine	intestine
32	chr1:47162400-47169800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:47162400-47170200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:47162400-47170600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:47162400-47170800	Weak transcription	Fetal Brain Male	brain
36	chr1:47162400-47171000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:47162600-47170800	Weak transcription	HSMMtube	muscle
38	chr1:47162800-47169600	Weak transcription	Hela-S3	cervix
39	chr1:47162800-47170000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:47162800-47170200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr1:47162800-47170200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:47162800-47170600	Weak transcription	HepG2	liver
43	chr1:47164000-47169800	Weak transcription	Fetal Stomach	stomach
44	chr1:47164000-47170800	Weak transcription	Lung	lung
45	chr1:47164200-47173600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:47164200-47177400	Strong transcription	GM12878-XiMat	blood
47	chr1:47164400-47182200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:47164400-47182800	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:47164600-47173400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:47164600-47181600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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