Variant report

Variant	rs2412412
Chromosome Location	chr15:39920140-39920141
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39871401..39883645-chr15:39918779..39926575,24	MCF-7	breast:
2	chr15:39920079..39920917-chr15:39960384..39961046,3	MCF-7	breast:
3	chr15:39887137..39895767-chr15:39912868..39924962,20	MCF-7	breast:
4	chr15:39913171..39923947-chr15:39954798..39966806,32	MCF-7	breast:
5	chr15:39920056..39920589-chr15:39960433..39961135,3	MCF-7	breast:
6	chr15:39873342..39875967-chr15:39918932..39920569,2	MCF-7	breast:
7	chr15:39920057..39920589-chr15:39960433..39961124,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction
ENSG00000150667	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10152640	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10520137	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs10520138	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10520142	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11070222	0.82[CHB][hapmap]
rs11070223	0.82[CHB][hapmap]
rs11070225	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs11070226	0.91[ASN][1000 genomes]
rs11070227	0.91[ASN][1000 genomes]
rs11070228	0.91[ASN][1000 genomes]
rs11630406	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11631820	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs11631824	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs11632117	0.88[ASN][1000 genomes]
rs11632879	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11635103	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11636823	0.88[ASN][1000 genomes]
rs11638041	0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs11638558	0.91[ASN][1000 genomes]
rs11852591	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11852649	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11855487	0.91[ASN][1000 genomes]
rs11856971	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11857819	0.85[CHB][hapmap]
rs12050804	0.84[CEU][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs12443011	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12900583	0.86[EUR][1000 genomes]
rs12908846	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1478604	1.00[CEU][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1478605	0.94[CEU][hapmap];0.80[CHB][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16969386	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs16969395	0.82[ASN][1000 genomes]
rs16969410	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs16969426	0.91[ASN][1000 genomes]
rs16969429	0.91[ASN][1000 genomes]
rs16969451	0.91[ASN][1000 genomes]
rs16969459	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs16969475	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs16969478	0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1876852	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1876853	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2169830	1.00[CEU][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2411310	0.92[TSI][hapmap];0.87[YRI][hapmap];0.88[EUR][1000 genomes]
rs2411313	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2411314	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2411315	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412413	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2412414	0.91[ASN][1000 genomes]
rs2412415	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2412416	0.91[ASN][1000 genomes]
rs2412417	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2412418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412419	0.82[CHB][hapmap]
rs2618162	0.94[CEU][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2618163	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2664139	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2664141	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2898686	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2898687	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs2898688	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2898962	0.91[ASN][1000 genomes]
rs4319738	0.88[EUR][1000 genomes]
rs4319740	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4349120	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4429263	0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs4479205	0.91[ASN][1000 genomes]
rs4493017	0.84[CEU][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes]
rs4505280	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs4526992	0.89[ASN][1000 genomes]
rs4547308	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4583211	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4628934	0.91[ASN][1000 genomes]
rs59449051	0.87[ASN][1000 genomes]
rs60164392	0.91[ASN][1000 genomes]
rs60195210	0.91[ASN][1000 genomes]
rs61130460	0.89[ASN][1000 genomes]
rs61439563	0.87[ASN][1000 genomes]
rs61568256	0.89[ASN][1000 genomes]
rs66781090	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7162070	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7162781	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7167184	0.91[ASN][1000 genomes]
rs7167366	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7168755	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7170335	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7176721	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7179293	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7179608	0.89[ASN][1000 genomes]
rs7180675	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72725079	0.91[ASN][1000 genomes]
rs72725080	0.91[ASN][1000 genomes]
rs72725084	0.91[ASN][1000 genomes]
rs72725093	0.87[ASN][1000 genomes]
rs72725101	0.87[ASN][1000 genomes]
rs768663	0.81[GIH][hapmap]
rs8026916	0.91[ASN][1000 genomes]
rs8029602	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs8032035	0.82[CHB][hapmap]
rs8032289	0.91[ASN][1000 genomes]
rs8034594	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8035354	0.84[EUR][1000 genomes]
rs8039035	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs884584	0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs949646	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs964424	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9806365	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs999393	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1048628	chr15:39877498-39940104	Enhancers Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1502	chr15:39884314-39928968	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	esv2753725	chr15:39918678-39921167	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2412412	CASC5	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39913200-39924000	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr15:39913400-39921000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:39913400-39922400	Enhancers	Fetal Intestine Large	intestine
4	chr15:39913400-39923800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:39914000-39922800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:39914200-39922600	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr15:39914600-39922800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr15:39914600-39923600	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr15:39914600-39923600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr15:39914600-39923800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr15:39914800-39923800	Enhancers	Primary T cells fromperipheralblood	blood
12	chr15:39916000-39922200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr15:39916000-39924000	Enhancers	HMEC	breast
14	chr15:39916200-39920800	Enhancers	Spleen	Spleen
15	chr15:39916200-39921000	Weak transcription	Thymus	Thymus
16	chr15:39916200-39922200	Enhancers	Left Ventricle	heart
17	chr15:39916200-39923400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:39916400-39937800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:39916600-39921000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:39916800-39921600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr15:39916800-39921800	Enhancers	Right Ventricle	heart
22	chr15:39917000-39920400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:39917400-39923800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:39917600-39920200	Weak transcription	Aorta	Aorta
25	chr15:39917600-39920400	Weak transcription	Psoas Muscle	Psoas
26	chr15:39917600-39920800	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:39917600-39921000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr15:39917600-39921600	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr15:39917600-39926200	Weak transcription	Esophagus	oesophagus
30	chr15:39917800-39920200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:39917800-39920200	Weak transcription	Liver	Liver
32	chr15:39917800-39920400	Weak transcription	HSMM	muscle
33	chr15:39917800-39920800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr15:39917800-39921200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:39918000-39920200	Weak transcription	Fetal Thymus	thymus
36	chr15:39918000-39920600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr15:39918000-39921200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:39918000-39921200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:39918000-39922200	Enhancers	HepG2	liver
40	chr15:39918200-39920600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:39918200-39920800	Weak transcription	Adipose Nuclei	Adipose
42	chr15:39918200-39921000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:39918200-39921000	Weak transcription	Brain Substantia Nigra	brain
44	chr15:39918200-39921400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:39918400-39921200	Weak transcription	NH-A	brain
46	chr15:39918400-39921600	Weak transcription	Osteobl	bone
47	chr15:39918400-39921800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:39918600-39920200	Weak transcription	NHLF	lung
49	chr15:39918600-39920600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:39918600-39920800	Weak transcription	NHEK	skin

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