Variant report

Variant	rs12650529
Chromosome Location	chr4:15645174-15645175
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15643577..15645460-chr4:15655132..15657368,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118564	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10005305	0.86[AFR][1000 genomes]
rs10008878	0.87[AFR][1000 genomes]
rs10009089	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015827	0.81[ASN][1000 genomes]
rs10017222	0.81[ASN][1000 genomes]
rs10025875	0.88[AFR][1000 genomes]
rs10034315	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10433813	0.81[ASN][1000 genomes]
rs11722757	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723478	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726647	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11732953	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12642407	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13134177	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13150957	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1786	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28394730	0.89[AFR][1000 genomes]
rs28402170	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28447067	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28644177	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28820655	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34473224	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34559117	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34955342	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35013326	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35120298	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3756247	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3775956	0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3775957	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4257653	0.96[ASN][1000 genomes]
rs4301111	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4331772	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4346644	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4396986	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4423870	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484296	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4549375	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4554069	0.89[AFR][1000 genomes]
rs4600905	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698116	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6414764	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449152	0.81[ASN][1000 genomes]
rs6815254	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6816982	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6823775	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6824422	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826058	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827406	0.81[ASN][1000 genomes]
rs6828776	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839654	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6843740	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6848779	0.87[AFR][1000 genomes]
rs6852735	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857442	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667175	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7698596	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9994518	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers 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	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv518830	chr4:15610771-15672200	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv521183	chr4:15610771-15692136	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv3464805	chr4:15643183-15646192	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3464806	chr4:15643188-15646159	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv3397107	chr4:15643237-15646120	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv3464807	chr4:15643251-15646118	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15568400-15655600	Weak transcription	Gastric	stomach
2	chr4:15600800-15653000	Weak transcription	Colonic Mucosa	Colon
3	chr4:15601000-15651600	Weak transcription	Small Intestine	intestine
4	chr4:15602600-15655600	Weak transcription	Pancreas	Pancrea
5	chr4:15605800-15650200	Weak transcription	Stomach Mucosa	stomach
6	chr4:15618600-15651000	Weak transcription	Spleen	Spleen
7	chr4:15622200-15655400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:15622600-15645800	Weak transcription	Aorta	Aorta
9	chr4:15626400-15646000	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr4:15627400-15645800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:15627400-15650000	Weak transcription	Fetal Heart	heart
12	chr4:15627400-15651200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:15627400-15652400	Weak transcription	Fetal Brain Male	brain
14	chr4:15627600-15645600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:15627600-15646800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr4:15627600-15650200	Weak transcription	Right Ventricle	heart
17	chr4:15628000-15655600	Weak transcription	Lung	lung
18	chr4:15628200-15645800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:15629600-15650400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr4:15633600-15646400	Strong transcription	Fetal Thymus	thymus
21	chr4:15634600-15646600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr4:15635000-15647000	Strong transcription	HSMM	muscle
23	chr4:15635600-15646400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:15635600-15655600	Weak transcription	Esophagus	oesophagus
25	chr4:15635800-15654800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:15636800-15651400	Weak transcription	Hela-S3	cervix
27	chr4:15638600-15645800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr4:15638600-15648600	Weak transcription	Ovary	ovary
29	chr4:15638600-15651400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr4:15638800-15647000	Weak transcription	Psoas Muscle	Psoas
31	chr4:15638800-15651600	Weak transcription	NHLF	lung
32	chr4:15638800-15655000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr4:15639000-15645600	Weak transcription	Brain Angular Gyrus	brain
34	chr4:15639000-15650800	Weak transcription	K562	blood
35	chr4:15640200-15645600	Weak transcription	Brain Substantia Nigra	brain
36	chr4:15640200-15646200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:15640400-15649600	Weak transcription	Brain Hippocampus Middle	brain
38	chr4:15640400-15651600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr4:15641200-15649400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:15641200-15649400	Weak transcription	GM12878-XiMat	blood
41	chr4:15641400-15647000	Weak transcription	Primary T cells from cord blood	blood
42	chr4:15641400-15650800	Weak transcription	A549	lung
43	chr4:15641600-15645600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:15641600-15651400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr4:15641800-15645800	Weak transcription	Brain Anterior Caudate	brain
46	chr4:15641800-15645800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr4:15641800-15649200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr4:15641800-15649200	Weak transcription	Colon Smooth Muscle	Colon
49	chr4:15641800-15649600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr4:15641800-15651400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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