Variant report

Variant	rs4069668
Chromosome Location	chr12:122415112-122415113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122414295..122416008-chr12:122423282..122426064,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BCL7A-3	chr12:122413670-122415137	l_748_chr12:122413669-122416306_testes

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10431199	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10840642	0.90[EUR][1000 genomes]
rs11043216	1.00[JPT][hapmap]
rs11043229	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap]
rs11043237	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11043242	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11043255	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11043263	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043276	1.00[MEX][hapmap]
rs11043277	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043285	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11043286	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11043290	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11043292	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11043295	0.97[ASN][1000 genomes]
rs11829607	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12230823	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610041	0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2707058	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap]
rs34768683	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847694	0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs56040016	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56122558	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56142842	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58326739	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59922210	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137708	0.83[CHB][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs7138296	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139277	1.00[MEX][hapmap]
rs7313252	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs73415674	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73415687	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73415696	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7958406	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7961660	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7971538	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7978386	0.95[EUR][1000 genomes];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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122375800-122415800	Weak transcription	Liver	Liver
2	chr12:122394000-122429800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:122396600-122439200	Weak transcription	Brain Anterior Caudate	brain
4	chr12:122403400-122417200	Weak transcription	NHDF-Ad	bronchial
5	chr12:122406200-122416800	Weak transcription	K562	blood
6	chr12:122406600-122418200	Weak transcription	Osteobl	bone
7	chr12:122409800-122427200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:122409800-122428400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:122409800-122428400	Weak transcription	NHEK	skin
10	chr12:122410000-122428600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:122411400-122416800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:122411400-122418000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:122411600-122415200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:122411600-122418200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:122411600-122418400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:122412800-122430600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr12:122413000-122417000	Weak transcription	Fetal Thymus	thymus
18	chr12:122413000-122417600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:122413200-122417000	Weak transcription	Thymus	Thymus
20	chr12:122413200-122417800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:122413200-122418000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:122413200-122428800	Weak transcription	HSMMtube	muscle
23	chr12:122413400-122417200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr12:122413600-122415400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:122414200-122415200	Strong transcription	Pancreas	Pancrea
26	chr12:122414600-122416600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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