Variant report

Variant	rs4400573
Chromosome Location	chr1:176077919-176077920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:176071649..176074006-chr1:176077683..176079750,2	K562	blood:
2	chr1:176077424..176078957-chr1:176081376..176083249,2	MCF-7	breast:
3	chr1:176074166..176076778-chr1:176077523..176081005,3	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]
rs12145778	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]
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]
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:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176028200-176079200	Weak transcription	HSMMtube	muscle
2	chr1:176046600-176082200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:176048800-176107000	Weak transcription	HepG2	liver
4	chr1:176054400-176131600	Weak transcription	NH-A	brain
5	chr1:176055000-176141600	Weak transcription	Hela-S3	cervix
6	chr1:176065600-176154800	Weak transcription	Aorta	Aorta
7	chr1:176066000-176081800	Weak transcription	GM12878-XiMat	blood
8	chr1:176068400-176079200	Weak transcription	Fetal Heart	heart
9	chr1:176068600-176087600	Weak transcription	NHLF	lung
10	chr1:176069000-176080800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:176069000-176090200	Weak transcription	Fetal Kidney	kidney
12	chr1:176069000-176116400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:176069000-176139200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:176069200-176082400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:176069200-176084400	Weak transcription	Psoas Muscle	Psoas
16	chr1:176069200-176087200	Weak transcription	Right Ventricle	heart
17	chr1:176069200-176123200	Weak transcription	Osteobl	bone
18	chr1:176069200-176126600	Weak transcription	HMEC	breast
19	chr1:176069200-176138800	Weak transcription	HUVEC	blood vessel
20	chr1:176069400-176121200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:176070200-176081400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:176070200-176087600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:176070400-176080800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:176070400-176082400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:176070400-176082800	Weak transcription	K562	blood
26	chr1:176070400-176083200	Weak transcription	Colonic Mucosa	Colon
27	chr1:176070400-176083200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:176070400-176084600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:176070400-176087400	Weak transcription	Brain Substantia Nigra	brain
30	chr1:176070400-176087600	Weak transcription	Spleen	Spleen
31	chr1:176070400-176091600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr1:176070400-176097800	Weak transcription	A549	lung
33	chr1:176070400-176107400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr1:176070400-176126400	Weak transcription	Brain Anterior Caudate	brain
35	chr1:176070400-176151400	Weak transcription	Pancreas	Pancrea
36	chr1:176070600-176082200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:176070600-176087800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:176070800-176079200	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:176070800-176102200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:176070800-176102600	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:176070800-176110600	Weak transcription	Small Intestine	intestine
42	chr1:176071000-176082800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr1:176071000-176082800	Weak transcription	Fetal Lung	lung
44	chr1:176071000-176085200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:176071000-176091600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:176071400-176079200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:176071400-176080800	Weak transcription	NHEK	skin
48	chr1:176071600-176086000	Strong transcription	Primary B cells from cord blood	blood
49	chr1:176071600-176088600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr1:176071600-176117800	Weak transcription	Gastric	stomach

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