Variant report

Variant	rs3747559
Chromosome Location	chr12:42718019-42718020
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr12:42717644-42721241	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:42630581..42632543-chr12:42717454..42720310,3	MCF-7	breast:
2	chr12:42536402..42539877-chr12:42717128..42721445,5	MCF-7	breast:
3	chr12:42537125..42540322-chr12:42717377..42722308,7	MCF-7	breast:
4	chr12:42629683..42634871-chr12:42717173..42721669,10	K562	blood:

Variant related genes	Relation type
PPHLN1	TF binding region
ENSG00000134283	Chromatin interaction
ENSG00000151233	Chromatin interaction
ENSG00000015153	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10160853	0.85[ASN][1000 genomes]
rs1037401	0.85[AMR][1000 genomes]
rs10506175	0.85[ASN][1000 genomes]
rs11181360	0.85[ASN][1000 genomes]
rs11181373	0.85[ASN][1000 genomes]
rs1139095	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11830387	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11832838	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12297206	0.88[ASN][1000 genomes]
rs12300188	0.88[ASN][1000 genomes]
rs12312515	0.85[ASN][1000 genomes]
rs12315471	0.85[ASN][1000 genomes]
rs12317772	0.85[ASN][1000 genomes]
rs12318401	0.85[ASN][1000 genomes]
rs17091061	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17091083	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17091094	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17091117	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17091138	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17091141	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17091163	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17091193	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17091220	0.80[AMR][1000 genomes]
rs17091226	0.85[AMR][1000 genomes]
rs17121217	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1962526	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1987127	0.90[ASN][1000 genomes]
rs2305423	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2406676	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2406677	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810787	0.95[EUR][1000 genomes]
rs3911246	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57447201	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57653125	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58594062	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59402225	0.88[EUR][1000 genomes]
rs59423833	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59501472	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59876649	0.83[ASN][1000 genomes]
rs60092940	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60287587	0.85[ASN][1000 genomes]
rs60598518	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60659836	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73114487	0.85[ASN][1000 genomes]
rs73116432	0.90[ASN][1000 genomes]
rs73116492	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73118486	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73118500	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73120410	0.88[EUR][1000 genomes]
rs73120468	0.88[EUR][1000 genomes]
rs73120476	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73120499	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73124406	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73124495	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73126404	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73126407	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73126412	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73126433	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73126453	0.90[AMR][1000 genomes]
rs73127418	0.85[ASN][1000 genomes]
rs73127421	0.81[ASN][1000 genomes]
rs73127428	0.84[ASN][1000 genomes]
rs73127435	0.81[ASN][1000 genomes]
rs73131138	0.85[ASN][1000 genomes]
rs7961228	0.85[EUR][1000 genomes];0.90[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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1048971	chr12:42651976-42801204	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
4	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 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	chr12:42693600-42719000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:42696200-42718800	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:42697000-42718800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr12:42699600-42718800	Weak transcription	HUVEC	blood vessel
5	chr12:42699800-42718200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:42701200-42718600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:42701800-42718600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:42701800-42718800	Weak transcription	Brain Angular Gyrus	brain
9	chr12:42701800-42719400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:42702200-42718600	Weak transcription	Brain Substantia Nigra	brain
11	chr12:42702600-42718800	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:42703800-42718800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:42704200-42718400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:42705200-42718600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:42705200-42718600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:42705200-42719000	Weak transcription	HSMMtube	muscle
17	chr12:42705400-42718400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:42705400-42719200	Weak transcription	Fetal Intestine Small	intestine
19	chr12:42705600-42719200	Weak transcription	Psoas Muscle	Psoas
20	chr12:42705600-42719400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr12:42705600-42719400	Weak transcription	Small Intestine	intestine
22	chr12:42705800-42718400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:42705800-42718600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:42705800-42719400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:42706000-42719400	Weak transcription	Aorta	Aorta
26	chr12:42706000-42719600	Weak transcription	Spleen	Spleen
27	chr12:42707000-42718600	Weak transcription	NHLF	lung
28	chr12:42707200-42718600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr12:42707600-42718600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:42707600-42718600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:42707800-42718400	Weak transcription	A549	lung
32	chr12:42707800-42718600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr12:42707800-42718600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr12:42707800-42718600	Weak transcription	HMEC	breast
35	chr12:42707800-42718800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:42707800-42718800	Weak transcription	NH-A	brain
37	chr12:42707800-42719200	Weak transcription	Right Ventricle	heart
38	chr12:42707800-42719400	Weak transcription	Colonic Mucosa	Colon
39	chr12:42708000-42718400	Weak transcription	NHEK	skin
40	chr12:42709000-42719400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:42709000-42719400	Weak transcription	Gastric	stomach
42	chr12:42709200-42718600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:42709400-42719400	Weak transcription	Esophagus	oesophagus
44	chr12:42709800-42718400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr12:42709800-42718600	Weak transcription	K562	blood
46	chr12:42710600-42718800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:42710800-42718600	Weak transcription	Brain Anterior Caudate	brain
48	chr12:42711000-42718400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr12:42711000-42718800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr12:42711000-42719200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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