Variant report

Variant	rs12202755
Chromosome Location	chr6:36884681-36884682
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36645356..36648241-chr6:36882559..36884793,2	MCF-7	breast:
2	chr6:36841727..36844418-chr6:36884410..36887065,2	K562	blood:
3	chr6:36880047..36886049-chr6:36952384..36956049,12	MCF-7	breast:
4	chr6:36882930..36885800-chr6:37137615..37140265,2	MCF-7	breast:
5	chr6:36882284..36884713-chr6:36895663..36897480,2	MCF-7	breast:
6	chr6:36884368..36885933-chr6:36886588..36889319,2	K562	blood:
7	chr6:36883006..36885868-chr6:36886588..36888530,2	K562	blood:
8	chr6:36872618..36878206-chr6:36882033..36886554,6	K562	blood:
9	chr6:36875857..36878206-chr6:36884249..36886554,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137409	Chromatin interaction
ENSG00000137168	Chromatin interaction
ENSG00000137193	Chromatin interaction
ENSG00000124762	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1022696	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap]
rs10456446	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1046578	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10498736	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10947638	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10947639	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10947640	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10947645	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10947647	0.85[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10947649	0.84[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs11757380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11759850	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11963298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11970506	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12110889	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12193721	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12194154	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12213087	0.90[GIH][hapmap]
rs12213912	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13190998	0.82[ASN][1000 genomes]
rs13199306	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13219894	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs13219913	0.81[ASN][1000 genomes]
rs13220210	0.81[ASN][1000 genomes]
rs16889252	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2272275	0.85[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2272276	0.85[ASW][hapmap];0.95[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2280675	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2293391	0.89[ASN][1000 genomes]
rs2293392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296932	0.83[ASN][1000 genomes]
rs2395663	0.85[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3074	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34453243	0.88[ASN][1000 genomes]
rs34605868	0.85[ASN][1000 genomes]
rs36048521	0.83[ASN][1000 genomes]
rs3734331	0.87[ASN][1000 genomes]
rs3734333	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3798469	0.83[CHB][hapmap]
rs3957238	0.90[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4475317	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4711473	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4711474	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4714023	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59892114	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61006307	0.81[ASN][1000 genomes]
rs61054996	0.82[ASN][1000 genomes]
rs6457964	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67540019	0.81[ASN][1000 genomes]
rs67854134	0.83[ASN][1000 genomes]
rs6901884	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6904504	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6918914	0.82[ASN][1000 genomes]
rs6920322	0.80[ASN][1000 genomes]
rs6932038	1.00[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6932175	0.85[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73418143	0.81[ASN][1000 genomes]
rs73420397	0.82[ASN][1000 genomes]
rs7741378	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7743646	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7743836	0.85[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7757241	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7761425	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7761653	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7770155	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7774420	0.85[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9296200	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9462233	0.87[ASN][1000 genomes]
rs9462236	0.82[ASN][1000 genomes]
rs9462238	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9462239	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9462240	0.85[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9462241	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9470429	0.82[ASN][1000 genomes]
rs9470434	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9470439	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9918461	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9969040	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs997674	0.83[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12202755	C6orf89	cis	cerebellum	SCAN
rs12202755	PNPLA1	cis	parietal	SCAN
rs12202755	C6orf89	Cis_1M	lymphoblastoid	RTeQTL
rs12202755	KCNK16	cis	parietal	SCAN
rs12202755	SFRS3	cis	lymphoblastoid	GTEx
rs12202755	C6orf89	cis	parietal	SCAN
rs12202755	C6orf1	cis	parietal	SCAN
rs12202755	LRFN2	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36854200-36887400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:36854400-36893000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:36866200-36896400	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:36867000-36897000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:36870800-36889400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:36871000-36888400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:36876000-36885000	Strong transcription	Fetal Stomach	stomach
8	chr6:36876200-36885800	Weak transcription	Psoas Muscle	Psoas
9	chr6:36876800-36885000	Weak transcription	Ovary	ovary
10	chr6:36876800-36885200	Weak transcription	Fetal Heart	heart
11	chr6:36877800-36896000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:36879400-36894000	Strong transcription	Fetal Brain Female	brain
13	chr6:36879600-36894000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:36879600-36895400	Strong transcription	Brain Germinal Matrix	brain
15	chr6:36879800-36885000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:36879800-36885000	Strong transcription	Left Ventricle	heart
17	chr6:36879800-36885200	Strong transcription	Right Ventricle	heart
18	chr6:36879800-36885400	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr6:36880000-36892000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr6:36880200-36884800	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:36880200-36887800	Strong transcription	Adipose Nuclei	Adipose
22	chr6:36880200-36893800	Strong transcription	K562	blood
23	chr6:36880400-36885400	Strong transcription	Lung	lung
24	chr6:36880400-36888000	Strong transcription	Brain Angular Gyrus	brain
25	chr6:36880600-36893600	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr6:36880600-36900000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:36880800-36889800	Strong transcription	Primary B cells from peripheral blood	blood
28	chr6:36881000-36892000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:36881000-36894800	Weak transcription	Fetal Brain Male	brain
30	chr6:36881200-36885000	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr6:36881200-36886400	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr6:36881200-36887200	Genic enhancers	Fetal Thymus	thymus
33	chr6:36881200-36889600	Strong transcription	Brain Hippocampus Middle	brain
34	chr6:36881400-36885800	Weak transcription	Esophagus	oesophagus
35	chr6:36881400-36893000	Strong transcription	Spleen	Spleen
36	chr6:36881400-36893600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:36881400-36893800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:36881400-36896200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:36881600-36889600	Strong transcription	Brain Cingulate Gyrus	brain
40	chr6:36881600-36891200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr6:36882000-36891600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr6:36882000-36893800	Strong transcription	Liver	Liver
43	chr6:36882200-36885000	Strong transcription	NHDF-Ad	bronchial
44	chr6:36882200-36885200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr6:36882200-36889200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr6:36882200-36891000	Strong transcription	Thymus	Thymus
47	chr6:36882200-36892000	Strong transcription	Brain Anterior Caudate	brain
48	chr6:36882200-36894000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr6:36882400-36885000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:36882400-36885000	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links