Variant report

Variant	rs7690329
Chromosome Location	chr4:152128294-152128295
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	chr4:152125993..152128805-chr4:152246228..152247794,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109686	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10000557	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10001039	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10005907	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10011421	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10016998	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10017154	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10020317	0.86[GIH][hapmap]
rs10030785	1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10032477	0.85[ASN][1000 genomes]
rs10213332	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10222881	1.00[JPT][hapmap]
rs1046168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10776521	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10776523	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10857253	0.86[GIH][hapmap]
rs10857254	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10857255	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10857256	0.90[ASN][1000 genomes]
rs10964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11099782	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11099783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11099787	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11099788	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11099790	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11099791	0.93[ASN][1000 genomes]
rs11099794	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099795	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723219	0.85[ASN][1000 genomes]
rs11726180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11729981	1.00[ASN][1000 genomes]
rs11730087	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733964	0.86[GIH][hapmap]
rs11734577	0.86[GIH][hapmap]
rs11734586	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11938266	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[ASN][1000 genomes]
rs11943477	1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12500168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12500223	1.00[ASN][1000 genomes]
rs12505974	0.86[GIH][hapmap]
rs12507657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13101417	0.86[GIH][hapmap]
rs13123932	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13125574	1.00[JPT][hapmap]
rs13145829	0.85[GIH][hapmap]
rs13146584	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13148755	0.81[ASN][1000 genomes]
rs13149045	1.00[ASN][1000 genomes]
rs1316364	1.00[ASN][1000 genomes]
rs1320006	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320007	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320192	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1875308	0.82[GIH][hapmap]
rs1878796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407167	0.82[GIH][hapmap]
rs2407168	0.85[GIH][hapmap]
rs2407220	0.81[GIH][hapmap]
rs2407221	0.82[GIH][hapmap]
rs2407406	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407411	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407414	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407415	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407424	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407425	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407426	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407427	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2407428	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407429	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407430	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2407439	0.85[ASN][1000 genomes]
rs2407440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2407441	0.81[ASN][1000 genomes]
rs2897657	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897659	0.86[GIH][hapmap]
rs2897660	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4434229	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4616734	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4640649	0.83[ASN][1000 genomes]
rs4696226	1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs4696229	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs4696235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696237	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4696648	1.00[JPT][hapmap]
rs4696658	0.86[GIH][hapmap]
rs6535763	1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs6535765	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6535766	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6535767	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6535775	0.95[ASN][1000 genomes]
rs6535776	1.00[ASN][1000 genomes]
rs6535777	0.81[ASN][1000 genomes]
rs6812695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6815608	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6819599	1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs6823953	1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825613	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6825952	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6826863	1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs6828937	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6833956	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6837905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6838301	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838845	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846323	0.86[GIH][hapmap]
rs6847669	1.00[ASN][1000 genomes]
rs6847927	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap]
rs6850311	0.82[GIH][hapmap]
rs6853215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6856569	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7659146	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.85[ASN][1000 genomes]
rs7664483	0.83[GIH][hapmap]
rs7666751	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668154	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7669180	0.86[GIH][hapmap]
rs7678748	1.00[JPT][hapmap]
rs7681030	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7683092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7687117	1.00[ASN][1000 genomes]
rs7689095	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7695005	1.00[ASN][1000 genomes]
rs938990	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv948719	chr4:151693149-152161625	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1016220	chr4:151997139-152164126	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv537306	chr4:151997139-152164126	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv870229	chr4:152114410-152161072	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152097200-152136600	Weak transcription	Colonic Mucosa	Colon
2	chr4:152097600-152128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:152098400-152147200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:152117600-152148800	Weak transcription	Esophagus	oesophagus
5	chr4:152118800-152146600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:152119000-152139400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:152119200-152129000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:152119400-152139400	Weak transcription	NHEK	skin
9	chr4:152120800-152153800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:152121000-152136400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:152121000-152138000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:152121200-152133800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:152123600-152128800	Enhancers	Fetal Lung	lung
14	chr4:152123600-152128800	Enhancers	HepG2	liver
15	chr4:152123600-152129200	Enhancers	Brain Hippocampus Middle	brain
16	chr4:152123600-152129400	Enhancers	Brain Substantia Nigra	brain
17	chr4:152124000-152129600	Enhancers	HUVEC	blood vessel
18	chr4:152124400-152128800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:152124400-152129600	Weak transcription	Gastric	stomach
20	chr4:152124400-152136400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:152124400-152139600	Weak transcription	Osteobl	bone
22	chr4:152124400-152147000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr4:152124600-152128600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:152124600-152128800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:152124600-152128800	Weak transcription	Pancreas	Pancrea
26	chr4:152124600-152136200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:152124600-152139400	Weak transcription	HSMM	muscle
28	chr4:152124600-152139600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:152124600-152139800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:152124600-152146800	Weak transcription	HSMMtube	muscle
31	chr4:152124800-152128800	Weak transcription	Fetal Intestine Small	intestine
32	chr4:152124800-152129600	Enhancers	Fetal Heart	heart
33	chr4:152124800-152136400	Weak transcription	NH-A	brain
34	chr4:152124800-152140000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:152125400-152129000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:152125400-152129000	Enhancers	Brain Angular Gyrus	brain
37	chr4:152125400-152129200	Enhancers	Brain Cingulate Gyrus	brain
38	chr4:152126000-152129400	Enhancers	Adipose Nuclei	Adipose
39	chr4:152126000-152129600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr4:152126200-152129600	Enhancers	Ovary	ovary
41	chr4:152126400-152128400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:152126400-152129200	Enhancers	Brain Anterior Caudate	brain
43	chr4:152126400-152129200	Enhancers	Colon Smooth Muscle	Colon
44	chr4:152126400-152147200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr4:152126800-152147000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr4:152127000-152129200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:152127000-152129400	Enhancers	A549	lung
48	chr4:152127200-152136400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:152127400-152128800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr4:152127600-152128600	Enhancers	Cortex derived primary cultured neurospheres	brain

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