Variant report

Variant	rs2502834
Chromosome Location	chr1:176066620-176066621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10158829	0.82[CHB][hapmap]
rs10494495	0.88[YRI][hapmap]
rs10494496	0.82[CHB][hapmap]
rs10737316	1.00[CHB][hapmap]
rs10753111	0.81[AMR][1000 genomes]
rs10753112	0.83[ASW][hapmap];0.88[YRI][hapmap]
rs10753117	0.83[ASW][hapmap];0.88[YRI][hapmap]
rs10798425	0.83[ASW][hapmap];0.88[YRI][hapmap]
rs10798427	1.00[CHB][hapmap];0.85[YRI][hapmap]
rs10798428	1.00[YRI][hapmap]
rs10798431	1.00[CHB][hapmap]
rs10798432	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs10798434	0.88[YRI][hapmap]
rs10798442	0.84[YRI][hapmap]
rs10913117	0.83[ASW][hapmap];0.88[YRI][hapmap]
rs10913150	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.90[ASN][1000 genomes]
rs1155229	0.82[AMR][1000 genomes]
rs11576471	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11806468	0.82[CHB][hapmap]
rs12029090	0.88[YRI][hapmap]
rs12239888	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs1357337	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[YRI][hapmap]
rs1522637	1.00[CHB][hapmap]
rs16849522	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs16849645	0.82[ASN][1000 genomes]
rs1770643	0.89[ASN][1000 genomes]
rs1831447	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs2039231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2039232	1.00[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs2481627	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2481634	1.00[ASN][1000 genomes]
rs2481639	0.81[ASN][1000 genomes]
rs2481641	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2481642	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2481647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs2481651	0.90[ASN][1000 genomes]
rs2481653	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs2481657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs2502822	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs2502824	1.00[CHB][hapmap]
rs2502826	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs2502830	0.95[ASN][1000 genomes]
rs2502832	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs2502835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502836	0.94[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs2502841	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2502842	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2502847	0.95[ASN][1000 genomes]
rs2861629	1.00[CHB][hapmap]
rs3845368	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs4129061	0.83[ASW][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.90[ASN][1000 genomes]
rs4304533	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs4409605	0.88[YRI][hapmap]
rs4543747	1.00[CHB][hapmap]
rs4603086	0.82[ASN][1000 genomes]
rs4650934	0.95[ASN][1000 genomes]
rs4652143	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs4652148	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs4652152	0.82[CHB][hapmap]
rs471534	0.92[ASN][1000 genomes]
rs533403	0.90[ASN][1000 genomes]
rs553852	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs559341	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs56367284	0.95[ASN][1000 genomes]
rs580978	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs58325269	0.81[ASN][1000 genomes]
rs598177	0.81[ASN][1000 genomes]
rs599326	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs602933	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs611883	0.95[ASN][1000 genomes]
rs61821029	0.95[ASN][1000 genomes]
rs6425367	0.82[AMR][1000 genomes]
rs6425368	1.00[CHB][hapmap];0.85[YRI][hapmap]
rs6678628	0.88[YRI][hapmap]
rs6678812	0.83[ASW][hapmap];0.88[YRI][hapmap]
rs6687043	0.94[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6688211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes]
rs6704509	1.00[CHB][hapmap];0.84[YRI][hapmap]
rs704825	0.81[ASN][1000 genomes]
rs704827	0.88[ASW][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[ASN][1000 genomes]
rs704830	0.85[CHB][hapmap]
rs704831	0.85[CHB][hapmap]
rs704832	0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7517351	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];0.85[YRI][hapmap]
rs7517503	0.83[ASW][hapmap]
rs7521561	1.00[CHB][hapmap]
rs7522442	1.00[CHB][hapmap]
rs7536464	1.00[CHB][hapmap]
rs7537480	0.88[AMR][1000 genomes]
rs7539247	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs7543769	1.00[CHB][hapmap]
rs7545043	1.00[CHB][hapmap];0.85[YRI][hapmap]
rs7546538	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7552181	1.00[CHB][hapmap];0.85[YRI][hapmap]
rs7553184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs791744	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs791795	0.83[ASN][1000 genomes]
rs791800	0.90[ASN][1000 genomes]
rs791801	0.94[ASW][hapmap];1.00[CHD][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.85[ASN][1000 genomes]
rs796933	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs9783047	1.00[CHB][hapmap];0.89[YRI][hapmap]

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:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175978400-176069000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:176028200-176079200	Weak transcription	HSMMtube	muscle
3	chr1:176035000-176069800	Weak transcription	NHEK	skin
4	chr1:176035200-176067600	Weak transcription	Colonic Mucosa	Colon
5	chr1:176035400-176067200	Weak transcription	HUVEC	blood vessel
6	chr1:176037200-176067200	Weak transcription	Small Intestine	intestine
7	chr1:176037200-176067400	Weak transcription	Osteobl	bone
8	chr1:176038600-176068800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:176039200-176068800	Weak transcription	HMEC	breast
10	chr1:176042800-176067200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:176046600-176082200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:176048400-176067600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:176048800-176107000	Weak transcription	HepG2	liver
14	chr1:176049200-176067200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:176050400-176067200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:176050400-176067200	Weak transcription	HSMM	muscle
17	chr1:176050400-176067200	Weak transcription	NHDF-Ad	bronchial
18	chr1:176052800-176068400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:176054400-176131600	Weak transcription	NH-A	brain
20	chr1:176055000-176141600	Weak transcription	Hela-S3	cervix
21	chr1:176058000-176070000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:176059400-176070200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:176059600-176068400	Weak transcription	Dnd41	blood
24	chr1:176060000-176067000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:176060200-176067200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:176060400-176067200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:176061200-176072800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:176062400-176072000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
29	chr1:176063200-176068800	Weak transcription	Spleen	Spleen
30	chr1:176064000-176067200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr1:176064000-176068800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:176064200-176066800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:176064400-176067000	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr1:176064400-176067000	ZNF genes & repeats	Ovary	ovary
35	chr1:176064400-176072800	ZNF genes & repeats	Primary T cells from cord blood	blood
36	chr1:176064400-176072800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:176064600-176066800	ZNF genes & repeats	Fetal Brain Female	brain
38	chr1:176064600-176067000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:176064600-176067000	ZNF genes & repeats	Fetal Stomach	stomach
40	chr1:176064600-176067000	ZNF genes & repeats	Lung	lung
41	chr1:176064600-176067000	ZNF genes & repeats	Pancreas	Pancrea
42	chr1:176064600-176067600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
43	chr1:176064600-176070400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:176064600-176072800	ZNF genes & repeats	Liver	Liver
45	chr1:176064800-176068600	Weak transcription	Right Ventricle	heart
46	chr1:176064800-176070400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:176065000-176068200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:176065000-176069800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr1:176065000-176071800	ZNF genes & repeats	Adipose Nuclei	Adipose
50	chr1:176065200-176066800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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