Variant report

Variant	rs7956314
Chromosome Location	chr12:46861668-46861669
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46859540..46862018-chr12:46919142..46921108,2	K562	blood:
2	chr12:46854831..46858483-chr12:46859173..46862265,4	MCF-7	breast:
3	chr12:46763112..46768883-chr12:46857331..46862698,8	K562	blood:
4	chr12:46852229..46855814-chr12:46857217..46861777,7	K562	blood:
5	chr12:46765375..46766918-chr12:46861342..46864304,2	MCF-7	breast:
6	chr12:46749620..46752358-chr12:46860774..46862635,2	MCF-7	breast:
7	chr12:46764216..46766970-chr12:46858797..46861757,2	K562	blood:
8	chr12:46859836..46862512-chr12:46864660..46866357,2	MCF-7	breast:
9	chr12:46857414..46859341-chr12:46861249..46864836,4	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC38A2-3	chr12:46861420-46861757	NONHSAT027883

No data

Variant related genes	Relation type
ENSG00000258096	Chromatin interaction
ENSG00000134294	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10748448	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10748450	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10785628	0.85[AMR][1000 genomes]
rs10785629	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10880973	0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10880974	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11183486	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11183500	0.90[YRI][hapmap]
rs11183502	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11183503	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11183504	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11837427	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12313929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12314541	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12824565	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs12827740	0.83[AMR][1000 genomes]
rs2252238	0.95[CEU][hapmap]
rs3925101	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4077707	0.85[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4077708	0.85[AMR][1000 genomes]
rs4768118	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs4768123	0.85[AMR][1000 genomes]
rs4768699	0.85[JPT][hapmap]
rs4768723	0.85[AMR][1000 genomes]
rs4768724	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4768725	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4768726	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768727	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768728	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768729	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768730	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768733	0.95[CEU][hapmap]
rs6582645	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs6582657	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6582658	0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6582659	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6582660	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6582661	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6582663	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7486915	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7488144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7488577	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7954645	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7959731	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7960808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7964767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7980455	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9669404	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs9706162	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9706460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9706520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9971879	0.91[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 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	chr12:46844600-46866000	Weak transcription	Fetal Intestine Large	intestine
2	chr12:46844600-46886000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:46853200-46867400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:46853800-46862600	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr12:46854800-46864000	Weak transcription	Spleen	Spleen
6	chr12:46854800-46866000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:46855000-46863800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr12:46855400-46863600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:46855400-46863800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:46855600-46863400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr12:46855800-46864000	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:46856000-46864000	Weak transcription	Right Ventricle	heart
13	chr12:46856000-46864800	Weak transcription	Small Intestine	intestine
14	chr12:46856000-46867800	Weak transcription	Aorta	Aorta
15	chr12:46856200-46862000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr12:46856200-46866000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr12:46856200-46866200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:46856200-46868200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:46856600-46867400	Weak transcription	Placenta	Placenta
20	chr12:46857000-46864000	Weak transcription	NHDF-Ad	bronchial
21	chr12:46857800-46864800	Weak transcription	Ovary	ovary
22	chr12:46858800-46867400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:46859000-46863200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:46859600-46862200	Weak transcription	Stomach Mucosa	stomach
25	chr12:46860000-46864000	Weak transcription	Right Atrium	heart
26	chr12:46860000-46866000	Weak transcription	K562	blood
27	chr12:46860000-46866200	Weak transcription	Fetal Intestine Small	intestine
28	chr12:46860200-46867400	Enhancers	Hela-S3	cervix
29	chr12:46860400-46864000	Weak transcription	Psoas Muscle	Psoas
30	chr12:46860800-46866800	Enhancers	HUVEC	blood vessel
31	chr12:46861000-46861800	Enhancers	Left Ventricle	heart
32	chr12:46861000-46862200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr12:46861000-46862600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:46861200-46862000	Weak transcription	HepG2	liver
35	chr12:46861200-46863400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:46861200-46863800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr12:46861200-46867000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:46861400-46862200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:46861400-46862400	Enhancers	Fetal Heart	heart
40	chr12:46861400-46863600	Weak transcription	Primary T cells from cord blood	blood
41	chr12:46861400-46866600	Enhancers	A549	lung
42	chr12:46861600-46862200	Weak transcription	NHEK	skin
43	chr12:46861600-46862600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr12:46861600-46863400	Weak transcription	Primary B cells from cord blood	blood
45	chr12:46861600-46863400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:46861600-46863600	Weak transcription	GM12878-XiMat	blood
47	chr12:46861600-46863800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr12:46861600-46864800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:46861600-46864800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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