Variant report

Variant	rs553852
Chromosome Location	chr1:176118738-176118739
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:176118719..176121398-chr1:176126586..176128691,2	MCF-7	breast:
2	chr1:176109806..176112763-chr1:176116214..176119123,3	K562	blood:
3	chr1:176117831..176119910-chr1:176126935..176128982,2	K562	blood:
4	chr1:176118538..176120169-chr1:176174472..176176395,2	MCF-7	breast:
5	chr1:176117419..176119853-chr1:176175222..176177852,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143207	Chromatin interaction
ENSG00000236021	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10158829	0.82[CHB][hapmap]
rs10494496	0.82[CHB][hapmap]
rs10494499	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs10737316	1.00[CHB][hapmap]
rs10798427	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes]
rs10798428	0.82[AMR][1000 genomes]
rs10798431	1.00[CHB][hapmap]
rs10798432	0.83[YRI][hapmap]
rs10798449	0.82[ASN][1000 genomes]
rs10913150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11576471	0.82[ASN][1000 genomes]
rs11801582	0.82[ASN][1000 genomes]
rs11806468	0.82[CHB][hapmap]
rs12038027	0.84[AMR][1000 genomes]
rs12239888	0.82[CHB][hapmap]
rs12403794	0.91[EUR][1000 genomes]
rs1357337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes]
rs1522637	1.00[CHB][hapmap]
rs16849522	0.82[CHB][hapmap]
rs16849645	0.87[ASN][1000 genomes]
rs16849697	0.82[ASN][1000 genomes]
rs16849735	1.00[JPT][hapmap]
rs17351808	0.91[CEU][hapmap]
rs17351933	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs17352072	0.84[EUR][1000 genomes]
rs17354252	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs1770643	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1831447	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs2039231	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2039232	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2136545	0.82[ASN][1000 genomes]
rs2481627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2481634	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2481635	0.91[EUR][1000 genomes]
rs2481639	0.81[ASN][1000 genomes]
rs2481641	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs2481647	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2481651	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2481653	1.00[CHB][hapmap]
rs2481657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2502822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2502824	1.00[CHB][hapmap]
rs2502826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2502830	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2502832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2502834	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2502835	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2502836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2502841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2502842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2502847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861629	1.00[CHB][hapmap]
rs2861630	0.91[CEU][hapmap]
rs3845368	0.82[CHB][hapmap]
rs4129061	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4304533	1.00[CHB][hapmap]
rs4307526	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4314844	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4460596	0.91[CEU][hapmap]
rs4543747	1.00[CHB][hapmap]
rs4603086	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4650934	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4650938	0.82[ASN][1000 genomes]
rs4652143	0.82[CHB][hapmap]
rs4652148	0.82[CHB][hapmap]
rs4652152	0.82[CHB][hapmap]
rs471534	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs533403	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs559341	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs56367284	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580978	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58325269	0.81[ASN][1000 genomes]
rs59276566	0.82[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]
rs60719126	0.88[EUR][1000 genomes]
rs611883	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61821007	0.88[EUR][1000 genomes]
rs61821009	0.88[EUR][1000 genomes]
rs61821028	0.91[EUR][1000 genomes]
rs61821029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61822662	0.84[EUR][1000 genomes]
rs6425368	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes]
rs6684747	0.86[AMR][1000 genomes]
rs6687043	0.84[YRI][hapmap]
rs6688211	1.00[CHB][hapmap];0.86[YRI][hapmap]
rs6704509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs704825	0.81[ASN][1000 genomes]
rs704827	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704830	0.85[CHB][hapmap]
rs704831	0.85[CHB][hapmap]
rs704832	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs74127185	0.89[EUR][1000 genomes]
rs7517351	0.81[AMR][1000 genomes]
rs7521561	1.00[CHB][hapmap]
rs7524972	0.83[AMR][1000 genomes]
rs7525001	1.00[JPT][hapmap]
rs7536464	1.00[CHB][hapmap]
rs7537435	0.84[AMR][1000 genomes]
rs7539247	1.00[CHB][hapmap];0.89[YRI][hapmap]
rs7543769	1.00[CHB][hapmap]
rs7545043	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes]
rs7545639	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7546538	0.85[ASN][1000 genomes]
rs7552181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes]
rs7553184	1.00[CHB][hapmap];0.90[YRI][hapmap]
rs7554913	0.91[CEU][hapmap]
rs791744	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs791795	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs791800	0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs791801	0.91[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs796933	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs9783047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.84[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:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176054400-176131600	Weak transcription	NH-A	brain
2	chr1:176055000-176141600	Weak transcription	Hela-S3	cervix
3	chr1:176065600-176154800	Weak transcription	Aorta	Aorta
4	chr1:176069000-176139200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:176069200-176123200	Weak transcription	Osteobl	bone
6	chr1:176069200-176126600	Weak transcription	HMEC	breast
7	chr1:176069200-176138800	Weak transcription	HUVEC	blood vessel
8	chr1:176069400-176121200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:176070400-176126400	Weak transcription	Brain Anterior Caudate	brain
10	chr1:176070400-176151400	Weak transcription	Pancreas	Pancrea
11	chr1:176072000-176140600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:176072800-176126600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:176076200-176126000	Weak transcription	Ovary	ovary
14	chr1:176076200-176127800	Weak transcription	Esophagus	oesophagus
15	chr1:176083000-176126000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:176085400-176142400	Weak transcription	Lung	lung
17	chr1:176085600-176122200	Weak transcription	Left Ventricle	heart
18	chr1:176085600-176122600	Weak transcription	Thymus	Thymus
19	chr1:176085600-176126000	Weak transcription	Fetal Stomach	stomach
20	chr1:176085600-176128600	Weak transcription	Placenta	Placenta
21	chr1:176087400-176122800	Weak transcription	NHEK	skin
22	chr1:176088600-176122800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:176090800-176126600	Weak transcription	Fetal Brain Male	brain
24	chr1:176093200-176119200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:176093200-176121200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:176094800-176126200	Weak transcription	Fetal Brain Female	brain
27	chr1:176094800-176126400	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:176095600-176130200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:176096000-176138800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:176100400-176126400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:176100800-176153200	Weak transcription	Colonic Mucosa	Colon
32	chr1:176101400-176126600	Weak transcription	Brain Substantia Nigra	brain
33	chr1:176102800-176121000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:176102800-176121800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:176102800-176126400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:176102800-176130000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:176102800-176130600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:176103000-176121000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:176103000-176125800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:176103200-176126600	Weak transcription	HSMMtube	muscle
41	chr1:176103400-176123400	Weak transcription	K562	blood
42	chr1:176103400-176126200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:176103400-176127400	Weak transcription	Fetal Heart	heart
44	chr1:176106000-176126400	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:176107600-176126600	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:176108000-176123200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr1:176108000-176124600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:176108000-176126600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:176108600-176129800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:176109800-176123400	Weak transcription	Brain Germinal Matrix	brain

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