Variant report

Variant	rs12144806
Chromosome Location	chr1:176134354-176134355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
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];0.83[EUR][1000 genomes]
rs12116561	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12119366	0.85[AMR][1000 genomes]
rs12121832	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12124916	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12125192	0.88[CEU][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12125328	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12127204	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs12127719	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12128099	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs12128327	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12129466	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12129873	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12130538	0.85[AMR][1000 genomes]
rs12132072	1.00[CEU][hapmap];0.92[AMR][1000 genomes]
rs12133268	0.85[AMR][1000 genomes]
rs12133310	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12133701	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12134392	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12134984	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12135045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12137136	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12139160	0.90[CEU][hapmap];0.85[AMR][1000 genomes]
rs12140631	0.85[AMR][1000 genomes]
rs12141054	0.85[AMR][1000 genomes]
rs12142010	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12142461	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12143425	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12144612	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12144692	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12145452	0.86[CEU][hapmap];0.85[AMR][1000 genomes]
rs12145703	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12145778	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12146072	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1330863	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16849475	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs4400573	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56230548	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7349083	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	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
5	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:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176055000-176141600	Weak transcription	Hela-S3	cervix
2	chr1:176065600-176154800	Weak transcription	Aorta	Aorta
3	chr1:176069000-176139200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:176069200-176138800	Weak transcription	HUVEC	blood vessel
5	chr1:176070400-176151400	Weak transcription	Pancreas	Pancrea
6	chr1:176072000-176140600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:176085400-176142400	Weak transcription	Lung	lung
8	chr1:176096000-176138800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:176100800-176153200	Weak transcription	Colonic Mucosa	Colon
10	chr1:176110600-176164000	Weak transcription	NHLF	lung
11	chr1:176111800-176139400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:176116000-176146200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:176122000-176139800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:176123800-176139800	Weak transcription	Fetal Kidney	kidney
15	chr1:176123800-176144200	Weak transcription	Left Ventricle	heart
16	chr1:176123800-176150000	Weak transcription	Osteobl	bone
17	chr1:176126400-176168800	Weak transcription	Small Intestine	intestine
18	chr1:176126800-176139800	Weak transcription	HSMMtube	muscle
19	chr1:176127000-176147000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:176127000-176174000	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:176127200-176137800	Weak transcription	HSMM	muscle
22	chr1:176127200-176153400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:176127400-176139200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:176127400-176139600	Weak transcription	Brain Anterior Caudate	brain
25	chr1:176127400-176140200	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:176127400-176141200	Weak transcription	HMEC	breast
27	chr1:176127400-176143200	Weak transcription	Brain Substantia Nigra	brain
28	chr1:176127400-176144200	Weak transcription	A549	lung
29	chr1:176127400-176153400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:176127400-176155400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:176127600-176138200	Weak transcription	Fetal Brain Male	brain
32	chr1:176127600-176138800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:176127600-176139200	Weak transcription	Fetal Brain Female	brain
34	chr1:176128000-176139600	Weak transcription	Psoas Muscle	Psoas
35	chr1:176128000-176144200	Weak transcription	Gastric	stomach
36	chr1:176128000-176147000	Weak transcription	Stomach Mucosa	stomach
37	chr1:176128000-176157800	Weak transcription	Spleen	Spleen
38	chr1:176128000-176175200	Weak transcription	Esophagus	oesophagus
39	chr1:176128200-176135800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr1:176128200-176136000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:176128200-176136200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:176128200-176138800	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:176128200-176139600	Weak transcription	Fetal Intestine Small	intestine
44	chr1:176128400-176134400	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr1:176128400-176154600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr1:176128600-176138800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:176128600-176147000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr1:176128600-176147200	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr1:176128600-176155600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:176128800-176152800	Weak transcription	Brain Cingulate Gyrus	brain

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