Variant report

Variant	rs4768699
Chromosome Location	chr12:46790392-46790393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46789348..46792000-chr12:46793237..46794849,2	K562	blood:
2	chr12:46788936..46790826-chr12:46823903..46825881,2	K562	blood:
3	chr12:46763985..46766407-chr12:46789016..46791282,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258096	Chromatin interaction
ENSG00000134294	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10748448	0.85[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10785628	0.82[CEU][hapmap]
rs10880967	0.85[ASN][1000 genomes]
rs10880973	0.82[CEU][hapmap];0.95[JPT][hapmap]
rs10880974	0.90[JPT][hapmap]
rs11183478	0.82[CEU][hapmap];0.94[GIH][hapmap]
rs11183479	0.82[CEU][hapmap]
rs11183483	0.82[CEU][hapmap];0.94[GIH][hapmap]
rs11183486	0.82[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap]
rs1125909	0.91[CEU][hapmap]
rs12313929	0.90[JPT][hapmap]
rs12314541	0.82[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12824565	0.82[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap]
rs1472178	0.82[CEU][hapmap];0.89[GIH][hapmap]
rs1492895	0.85[ASN][1000 genomes]
rs2131371	0.82[CEU][hapmap];0.89[GIH][hapmap]
rs2220727	0.85[ASN][1000 genomes]
rs2408498	0.85[ASN][1000 genomes]
rs2897951	0.82[CEU][hapmap];0.85[ASN][1000 genomes]
rs3936214	0.81[CEU][hapmap]
rs4077707	0.82[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap]
rs4077708	0.82[CEU][hapmap];0.89[GIH][hapmap]
rs4258438	0.86[CEU][hapmap]
rs4427617	0.86[CEU][hapmap]
rs4768118	0.87[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap]
rs4768123	0.82[CEU][hapmap];0.89[GIH][hapmap]
rs4768700	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768701	0.86[AMR][1000 genomes]
rs4768702	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4768703	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768709	0.82[CEU][hapmap]
rs4768710	0.85[ASN][1000 genomes]
rs4768711	0.84[ASN][1000 genomes]
rs4768712	0.85[ASN][1000 genomes]
rs4768713	0.85[ASN][1000 genomes]
rs4768714	0.84[ASN][1000 genomes]
rs4768716	0.82[CEU][hapmap];0.89[GIH][hapmap]
rs4768723	0.82[CEU][hapmap];0.89[GIH][hapmap]
rs4768727	0.90[JPT][hapmap]
rs4768730	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs6582636	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6582645	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6582656	0.81[MEX][hapmap]
rs6582657	0.82[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs6582658	0.82[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs6582661	0.89[JPT][hapmap]
rs6582663	0.90[JPT][hapmap]
rs7134505	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7486915	0.90[JPT][hapmap]
rs7488144	0.90[JPT][hapmap]
rs7953450	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954645	0.90[JPT][hapmap]
rs7956314	0.85[JPT][hapmap]
rs7959731	0.82[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap]
rs7960808	0.90[JPT][hapmap]
rs7964767	0.90[JPT][hapmap]
rs9669404	0.82[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9706460	0.90[JPT][hapmap]
rs9706520	0.90[JPT][hapmap]
rs9971879	0.82[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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	chr12:46778800-46797200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:46779600-46802800	Weak transcription	Pancreas	Pancrea
3	chr12:46781600-46795400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:46781800-46795000	Weak transcription	Fetal Muscle Leg	muscle
5	chr12:46782000-46794600	Weak transcription	Fetal Kidney	kidney
6	chr12:46782000-46794600	Weak transcription	Placenta	Placenta
7	chr12:46782000-46794600	Weak transcription	Psoas Muscle	Psoas
8	chr12:46782400-46792600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:46782800-46796600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr12:46783000-46794200	Weak transcription	Thymus	Thymus
11	chr12:46783200-46790800	Weak transcription	Ovary	ovary
12	chr12:46783200-46795600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:46783200-46796200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:46783200-46796600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr12:46783200-46796800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:46783400-46794600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr12:46783400-46795000	Weak transcription	Fetal Heart	heart
18	chr12:46783400-46795400	Weak transcription	HSMM	muscle
19	chr12:46783400-46796200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:46784200-46791800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr12:46785000-46796200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:46785200-46793800	Weak transcription	Dnd41	blood
23	chr12:46785200-46794400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr12:46785200-46795000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:46785200-46796000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr12:46785400-46795200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr12:46785600-46794400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:46785600-46796600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:46785800-46796600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr12:46786600-46796000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr12:46786800-46791200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:46786800-46794200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:46786800-46794200	Weak transcription	Primary T cells from cord blood	blood
34	chr12:46786800-46794200	Weak transcription	Fetal Thymus	thymus
35	chr12:46786800-46794200	Weak transcription	Osteobl	bone
36	chr12:46786800-46794400	Weak transcription	NHDF-Ad	bronchial
37	chr12:46787000-46790400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr12:46787000-46795200	Weak transcription	Fetal Lung	lung
39	chr12:46787000-46795400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:46787000-46798400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:46787200-46794400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:46787400-46795600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:46787800-46798200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:46788400-46794400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:46789200-46795400	Weak transcription	Fetal Brain Male	brain
46	chr12:46789600-46790800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr12:46789600-46790800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr12:46789600-46794400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:46789600-46795200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr12:46789600-46796800	Weak transcription	Primary hematopoietic stem cells	blood

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