Variant report

Variant	rs10176342
Chromosome Location	chr2:54333078-54333079
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10166363	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169648	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10172916	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10192403	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10205315	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208690	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11125521	0.93[GIH][hapmap]
rs11675345	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676433	1.00[ASN][1000 genomes]
rs11677951	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11687470	1.00[ASN][1000 genomes]
rs11688581	1.00[ASN][1000 genomes]
rs11695936	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891079	0.93[GIH][hapmap]
rs13394575	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs13418039	0.91[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13418658	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13418839	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429859	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1559039	0.91[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1559040	0.91[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17045513	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17189638	1.00[ASN][1000 genomes]
rs2112125	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28368466	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28416116	1.00[ASN][1000 genomes]
rs34433964	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs35641543	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55666400	1.00[ASN][1000 genomes]
rs55672362	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55820614	1.00[ASN][1000 genomes]
rs56374740	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61572658	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721034	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67951010	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72799283	1.00[ASN][1000 genomes]
rs72799301	1.00[ASN][1000 genomes]
rs72800709	1.00[ASN][1000 genomes]
rs72800719	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800725	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800729	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800732	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800738	1.00[ASN][1000 genomes]
rs72800739	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800741	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800746	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800751	0.91[EUR][1000 genomes]
rs72800752	1.00[ASN][1000 genomes]
rs72800759	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800765	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800772	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800775	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561836	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7571660	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586592	0.83[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs998381	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1010175	chr2:54292951-54343466	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv1851003	chr2:54324701-54372931	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
11	nsv1007731	chr2:54331179-54452329	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
12	nsv535723	chr2:54331179-54452329	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:54324000-54333400	Enhancers	Primary B cells from cord blood	blood
3	chr2:54324000-54334400	Enhancers	Primary B cells from peripheral blood	blood
4	chr2:54325800-54334400	Weak transcription	Brain Angular Gyrus	brain
5	chr2:54326000-54334000	Weak transcription	Brain Substantia Nigra	brain
6	chr2:54331200-54335000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:54331200-54342000	Weak transcription	Psoas Muscle	Psoas
8	chr2:54331200-54342400	Weak transcription	Pancreas	Pancrea
9	chr2:54331400-54333600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:54331400-54333600	Weak transcription	K562	blood
11	chr2:54331400-54334000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr2:54331400-54334000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:54331400-54334000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:54331400-54334000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr2:54331400-54334000	Weak transcription	Brain Anterior Caudate	brain
16	chr2:54331400-54334000	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:54331400-54334000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:54331400-54334000	Weak transcription	Thymus	Thymus
19	chr2:54331400-54334000	Weak transcription	HSMMtube	muscle
20	chr2:54331400-54334400	Weak transcription	Adipose Nuclei	Adipose
21	chr2:54331400-54334400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr2:54331400-54334600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:54331400-54334800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:54331400-54334800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:54331400-54335000	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:54331400-54335200	Weak transcription	Fetal Heart	heart
27	chr2:54331400-54335400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:54331400-54335800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr2:54331400-54335800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:54331400-54342200	Weak transcription	Aorta	Aorta
31	chr2:54331600-54334000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:54331600-54334000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:54331600-54334200	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:54331600-54334200	Weak transcription	HUVEC	blood vessel
35	chr2:54331600-54334600	Weak transcription	NHDF-Ad	bronchial
36	chr2:54331600-54335000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:54331800-54334000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr2:54331800-54334400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:54331800-54335000	Weak transcription	NHEK	skin
40	chr2:54332000-54333600	Weak transcription	A549	lung
41	chr2:54332000-54333800	Weak transcription	HepG2	liver
42	chr2:54332000-54334000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr2:54332000-54334200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr2:54332000-54335200	Weak transcription	HMEC	breast
45	chr2:54332200-54334000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:54332400-54333600	Weak transcription	Liver	Liver
47	chr2:54332400-54334000	Weak transcription	Hela-S3	cervix
48	chr2:54332400-54334800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:54332400-54335000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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