Variant report

Variant	rs12145778
Chromosome Location	chr1:176090177-176090178
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:176082187..176085004-chr1:176089013..176091231,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10494497	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12116561	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12119366	0.85[AMR][1000 genomes]
rs12121832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12124916	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12125192	0.88[CEU][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12125328	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12127204	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs12127719	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12128099	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs12128327	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12129466	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12129873	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12130538	0.85[AMR][1000 genomes]
rs12132072	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12133268	0.85[AMR][1000 genomes]
rs12133310	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12133701	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12134392	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12134984	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12135045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12137136	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12139160	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs12140631	0.85[AMR][1000 genomes]
rs12141054	0.85[AMR][1000 genomes]
rs12142010	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12142461	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12143425	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12144612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12144692	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12144806	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12145452	0.85[CEU][hapmap];0.85[AMR][1000 genomes]
rs12145703	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12146072	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1330863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16849475	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs4400573	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56230548	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7349083	0.86[AFR][1000 genomes];0.85[AMR][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	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872561	chr1:175949646-176092167	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv872564	chr1:176027978-176102808	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv548246	chr1:176043797-176136273	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv872565	chr1:176058782-176172795	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176048800-176107000	Weak transcription	HepG2	liver
2	chr1:176054400-176131600	Weak transcription	NH-A	brain
3	chr1:176055000-176141600	Weak transcription	Hela-S3	cervix
4	chr1:176065600-176154800	Weak transcription	Aorta	Aorta
5	chr1:176069000-176090200	Weak transcription	Fetal Kidney	kidney
6	chr1:176069000-176116400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:176069000-176139200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:176069200-176123200	Weak transcription	Osteobl	bone
9	chr1:176069200-176126600	Weak transcription	HMEC	breast
10	chr1:176069200-176138800	Weak transcription	HUVEC	blood vessel
11	chr1:176069400-176121200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:176070400-176091600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:176070400-176097800	Weak transcription	A549	lung
14	chr1:176070400-176107400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:176070400-176126400	Weak transcription	Brain Anterior Caudate	brain
16	chr1:176070400-176151400	Weak transcription	Pancreas	Pancrea
17	chr1:176070800-176102200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:176070800-176102600	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:176070800-176110600	Weak transcription	Small Intestine	intestine
20	chr1:176071000-176091600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:176071600-176117800	Weak transcription	Gastric	stomach
22	chr1:176072000-176140600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:176072400-176108600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:176072600-176107400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:176072800-176114600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:176072800-176114800	Weak transcription	NHDF-Ad	bronchial
27	chr1:176072800-176126600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:176076200-176102000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:176076200-176126000	Weak transcription	Ovary	ovary
30	chr1:176076200-176127800	Weak transcription	Esophagus	oesophagus
31	chr1:176079800-176105400	Weak transcription	Colon Smooth Muscle	Colon
32	chr1:176080000-176103400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:176081200-176114800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:176083000-176126000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:176083400-176091000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:176083400-176094600	Weak transcription	Fetal Lung	lung
37	chr1:176083600-176091400	Weak transcription	K562	blood
38	chr1:176083600-176102600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:176083800-176106200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:176084200-176091400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:176084400-176094600	Weak transcription	Primary T cells from cord blood	blood
42	chr1:176084800-176095200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:176085000-176101200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:176085400-176091400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:176085400-176091400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr1:176085400-176096400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:176085400-176142400	Weak transcription	Lung	lung
48	chr1:176085600-176091200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:176085600-176091400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:176085600-176091400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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