Variant report

Variant	rs10166363
Chromosome Location	chr2:54330242-54330243
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54329359..54330891-chr2:54348724..54350959,2	MCF-7	breast:
2	chr2:54330146..54332373-chr2:54340352..54345020,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10169648	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10172916	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176342	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176406	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10192403	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10205315	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208690	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
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	0.81[AMR][1000 genomes]
rs13394575	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13418039	0.91[CEU][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13418658	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13418839	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429859	0.89[AFR][1000 genomes];0.89[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];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17045513	0.87[AFR][1000 genomes];0.80[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	0.87[AFR][1000 genomes];0.80[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];0.95[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	0.98[AFR][1000 genomes];0.98[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	0.85[AFR][1000 genomes];0.80[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:10 , 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

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54280800-54331000	Weak transcription	Aorta	Aorta
2	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:54318200-54330800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:54318200-54331000	Weak transcription	Brain Anterior Caudate	brain
5	chr2:54320400-54331000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:54321800-54330800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:54321800-54331000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr2:54324000-54333400	Enhancers	Primary B cells from cord blood	blood
9	chr2:54324000-54334400	Enhancers	Primary B cells from peripheral blood	blood
10	chr2:54325400-54330400	Weak transcription	HUVEC	blood vessel
11	chr2:54325800-54334400	Weak transcription	Brain Angular Gyrus	brain
12	chr2:54326000-54334000	Weak transcription	Brain Substantia Nigra	brain
13	chr2:54326600-54330800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:54327200-54330800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:54327200-54330800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:54327400-54331000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr2:54327400-54331000	Weak transcription	K562	blood
18	chr2:54327600-54331000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:54328400-54330800	Weak transcription	GM12878-XiMat	blood
20	chr2:54328400-54331200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:54329000-54332400	Enhancers	Hela-S3	cervix
22	chr2:54329200-54330600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:54329400-54331600	Enhancers	NHDF-Ad	bronchial
24	chr2:54329600-54330600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:54329800-54331400	Enhancers	Osteobl	bone
26	chr2:54329800-54332000	Enhancers	HMEC	breast
27	chr2:54330000-54331000	Enhancers	A549	lung
28	chr2:54330000-54331400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:54330000-54331400	Enhancers	NHLF	lung
30	chr2:54330000-54331600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:54330000-54331800	Enhancers	NHEK	skin
32	chr2:54330000-54332400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:54330200-54331000	Weak transcription	HSMMtube	muscle
34	chr2:54330200-54332400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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