Variant report

Variant	rs2811593
Chromosome Location	chr1:93343891-93343892
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	chr1:93342948..93345032-chr1:93349007..93351631,2	K562	blood:

Extended variants
information (count: 110 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10493863	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10782945	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10782946	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10874744	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10874746	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10874747	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10874751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10874753	0.92[CEU][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs11164830	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164836	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11164840	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164842	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11164843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164844	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11164845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11423955	0.92[ASN][1000 genomes]
rs11577636	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11578986	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11583491	0.80[EUR][1000 genomes]
rs11586570	0.87[MKK][hapmap]
rs11587920	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12060952	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12065253	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069727	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12074608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081675	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs12745968	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1360366	0.96[CEU][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17380908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2065915	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs2255717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255723	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263247	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2481711	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481712	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481713	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs2481714	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2492292	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2492293	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2492294	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2774941	0.90[CHD][hapmap]
rs2774945	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2774946	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2774949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2774950	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2774952	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2774953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2774954	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2774955	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2774956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2811589	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2811590	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2811591	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2811594	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2811596	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2811597	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2811598	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2811599	0.90[CHD][hapmap]
rs2811600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2811602	0.81[CHD][hapmap]
rs2893225	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34084844	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34389767	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34398175	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35183060	0.92[MKK][hapmap]
rs35367625	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35807969	0.80[EUR][1000 genomes]
rs4300228	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4308991	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4351651	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4420089	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4450029	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4561051	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4592265	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4847223	0.86[AMR][1000 genomes]
rs4847378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4847384	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56193705	0.80[EUR][1000 genomes]
rs6604028	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6604029	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6604030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6604031	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6659942	0.81[CHD][hapmap]
rs6694051	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6697543	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6698082	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6698179	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700585	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7417198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7515257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7517935	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7521417	0.85[MKK][hapmap]
rs7536563	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7542608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7543964	0.90[CHD][hapmap]
rs7550347	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7550660	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9439948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9440127	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9440134	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs949915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9651257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv508393	chr1:93290513-93344924	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2811593	KIAA1107	cis	cerebellum	SCAN
rs2811593	MTF2	cis	cerebellum	SCAN
rs2811593	BARHL2	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93304400-93349000	Weak transcription	Aorta	Aorta
2	chr1:93325200-93348400	Weak transcription	NHEK	skin
3	chr1:93333000-93348600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:93335800-93348400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:93336400-93348800	Weak transcription	Left Ventricle	heart
6	chr1:93336600-93349200	Weak transcription	HepG2	liver
7	chr1:93337000-93348400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:93337800-93345200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:93338800-93347800	Weak transcription	HMEC	breast
10	chr1:93338800-93348200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:93338800-93348400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:93339000-93345000	Weak transcription	A549	lung
13	chr1:93339000-93348200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr1:93339000-93352600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:93340800-93348800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:93340800-93351600	Weak transcription	Small Intestine	intestine
17	chr1:93341800-93344200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:93341800-93345600	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr1:93342000-93344000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr1:93342000-93344000	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr1:93342000-93344200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr1:93342000-93345800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:93342200-93344200	Flanking Active TSS	Dnd41	blood
24	chr1:93342400-93344000	Enhancers	Brain Germinal Matrix	brain
25	chr1:93342600-93344200	Enhancers	Primary B cells from cord blood	blood
26	chr1:93342800-93344000	Enhancers	Primary B cells from peripheral blood	blood
27	chr1:93343000-93344000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:93343000-93344000	Enhancers	Adipose Nuclei	Adipose
29	chr1:93343000-93344000	Enhancers	Fetal Brain Female	brain
30	chr1:93343000-93345600	Enhancers	Fetal Thymus	thymus
31	chr1:93343200-93344000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:93343200-93345800	Enhancers	Primary T cells fromperipheralblood	blood
33	chr1:93343400-93345400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:93343400-93348400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:93343600-93344000	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr1:93343600-93344000	Enhancers	Liver	Liver
37	chr1:93343600-93344000	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr1:93343600-93344000	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr1:93343600-93344000	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr1:93343600-93344000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr1:93343600-93344400	Enhancers	Primary T cells from cord blood	blood
42	chr1:93343600-93344400	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr1:93343600-93344800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:93343600-93344800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:93343600-93345000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:93343600-93345200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:93343600-93345800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr1:93343800-93344000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:93343800-93344000	Enhancers	Brain Angular Gyrus	brain
50	chr1:93343800-93344000	Enhancers	Brain Cingulate Gyrus	brain

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