Variant report

Variant	rs7953339
Chromosome Location	chr12:46868900-46868901
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46763709..46766577-chr12:46865824..46870117,4	K562	blood:
2	chr12:46865906..46867668-chr12:46868121..46870564,2	K562	blood:
3	chr12:46867765..46869816-chr12:46873759..46876324,2	K562	blood:
4	chr12:46857526..46859603-chr12:46866422..46869181,2	MCF-7	breast:
5	chr12:46868625..46870317-chr12:46878196..46880801,2	MCF-7	breast:
6	chr12:46850488..46852109-chr12:46868187..46870215,2	MCF-7	breast:
7	chr12:46775882..46782891-chr12:46867252..46874732,11	MCF-7	breast:
8	chr12:46848032..46851885-chr12:46865278..46868911,4	MCF-7	breast:
9	chr12:46853187..46855713-chr12:46867709..46870623,2	K562	blood:
10	chr12:46764487..46767688-chr12:46865633..46870599,8	MCF-7	breast:
11	chr12:46865908..46869326-chr12:46872874..46876694,4	MCF-7	breast:
12	chr12:46750575..46752943-chr12:46867557..46871198,3	K562	blood:
13	chr12:46867596..46869336-chr12:46885001..46888174,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258096	Chromatin interaction
ENSG00000257261	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000257496	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10467215	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11183454	0.82[CHB][hapmap]
rs11183467	0.94[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap]
rs11183482	0.94[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap]
rs11183500	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11183510	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11183512	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11183513	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1125908	0.81[CHB][hapmap];0.89[CHD][hapmap]
rs12296535	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12296783	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12299499	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs12302091	0.81[ASN][1000 genomes]
rs12313929	0.92[YRI][hapmap]
rs12317179	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12317255	0.94[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12321468	0.82[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap]
rs12321512	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs12321960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13377959	0.94[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs17096884	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs17096896	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs17096922	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs17096998	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2307062	0.82[CHB][hapmap]
rs2307063	0.82[CHB][hapmap]
rs34098443	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs36010856	0.95[ASN][1000 genomes]
rs3742061	0.82[CHB][hapmap]
rs3935048	0.82[ASW][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]
rs4768727	1.00[YRI][hapmap]
rs58127062	0.92[ASN][1000 genomes]
rs58353248	0.92[ASN][1000 genomes]
rs58890669	0.95[ASN][1000 genomes]
rs59608605	0.95[ASN][1000 genomes]
rs6582661	0.91[YRI][hapmap]
rs7313172	0.92[ASN][1000 genomes]
rs73290315	0.95[ASN][1000 genomes]
rs7486915	0.88[YRI][hapmap]
rs7954314	0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs7954645	0.88[YRI][hapmap]
rs7960808	0.88[YRI][hapmap]
rs7967889	0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7980023	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

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:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46844600-46886000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:46864200-46877400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr12:46864400-46877400	Weak transcription	Primary T cells from cord blood	blood
4	chr12:46865400-46870200	Weak transcription	Lung	lung
5	chr12:46865400-46879200	Weak transcription	Right Ventricle	heart
6	chr12:46866400-46871000	Weak transcription	Gastric	stomach
7	chr12:46866400-46871400	Weak transcription	Dnd41	blood
8	chr12:46867800-46871600	Weak transcription	Fetal Thymus	thymus
9	chr12:46867800-46873400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:46867800-46875800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:46868000-46869200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:46868000-46869400	Enhancers	Hela-S3	cervix
13	chr12:46868000-46872200	Enhancers	HepG2	liver
14	chr12:46868000-46876200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:46868000-46876200	Weak transcription	Primary B cells from cord blood	blood
16	chr12:46868000-46876400	Weak transcription	K562	blood
17	chr12:46868000-46881200	Weak transcription	GM12878-XiMat	blood
18	chr12:46868000-46883200	Weak transcription	Fetal Heart	heart
19	chr12:46868200-46869000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:46868200-46869200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:46868200-46869200	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr12:46868200-46869200	Enhancers	HUVEC	blood vessel
23	chr12:46868200-46869600	Enhancers	A549	lung
24	chr12:46868200-46871000	Weak transcription	NHLF	lung
25	chr12:46868200-46877400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:46868200-46879200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr12:46868400-46871200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr12:46868600-46869600	Weak transcription	Aorta	Aorta
29	chr12:46868600-46869800	Weak transcription	Placenta	Placenta
30	chr12:46868600-46870000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:46868600-46870000	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:46868600-46870200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:46868600-46870200	Weak transcription	Esophagus	oesophagus
34	chr12:46868600-46870200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:46868600-46870400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:46868600-46871000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:46868600-46871000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:46868600-46871200	Weak transcription	Osteobl	bone
39	chr12:46868600-46872400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr12:46868600-46872600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr12:46868600-46872800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:46868600-46874000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:46868600-46874000	Weak transcription	Pancreas	Pancrea
44	chr12:46868600-46874000	Weak transcription	NHDF-Ad	bronchial
45	chr12:46868600-46874000	Weak transcription	NHEK	skin
46	chr12:46868600-46874200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:46868600-46877400	Weak transcription	Fetal Intestine Small	intestine
48	chr12:46868600-46877400	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr12:46868600-46877600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:46868600-46877600	Weak transcription	Ovary	ovary

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