Variant report

Variant	rs3736740
Chromosome Location	chr6:88117014-88117015
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	chr6:88116849..88119599-chr6:88181543..88183591,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164414	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1051550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11964198	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11964212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11964237	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11966859	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203156	0.92[JPT][hapmap]
rs12529410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12529423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12661245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12663865	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13211410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13211836	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13217485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs242291	0.92[JPT][hapmap]
rs34977536	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35332886	0.94[ASN][1000 genomes]
rs35869302	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4329082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707365	0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4707367	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4707368	0.94[ASN][1000 genomes]
rs4707369	0.92[ASN][1000 genomes]
rs4707370	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4707371	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4707372	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5009694	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6454610	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6454611	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6454612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6454613	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6454614	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6454615	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6454616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6454617	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6454618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6454621	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6454622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs6454623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs6454624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6454625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs6454626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs6899561	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6900397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6906433	0.91[CEU][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6907825	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6909168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6910429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912282	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6912300	0.94[ASN][1000 genomes]
rs6912442	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6912875	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6915562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6919775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6920937	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6940716	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs71541172	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7744338	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7744793	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7746469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7749047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7749162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753821	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7760108	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761462	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7764266	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764963	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7766462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7773262	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9294378	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9342112	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9344708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9353484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9353485	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9353486	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9353487	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9353488	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9362428	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9444493	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444494	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9444495	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9444496	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450672	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9450674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450682	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3736740	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs3736740	C6orf164	cis	lung	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88106400-88117200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:88106400-88117200	Weak transcription	Fetal Muscle Leg	muscle
3	chr6:88116800-88117200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
4	chr6:88116800-88117200	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr6:88116800-88117200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr6:88116800-88117400	Flanking Active TSS	HUVEC	blood vessel
7	chr6:88116800-88117600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:88116800-88118400	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr6:88116800-88118600	Active TSS	Muscle Satellite Cultured Cells	--
10	chr6:88116800-88118800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:88116800-88119000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:88116800-88119000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:88116800-88119000	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr6:88116800-88119000	Active TSS	NHDF-Ad	bronchial
15	chr6:88117000-88117200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:88117000-88117200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
17	chr6:88117000-88117200	Bivalent/Poised TSS	Primary B cells from cord blood	blood
18	chr6:88117000-88117200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:88117000-88117200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:88117000-88117200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:88117000-88117200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr6:88117000-88117200	Enhancers	Liver	Liver
23	chr6:88117000-88117200	Flanking Active TSS	Brain Cingulate Gyrus	brain
24	chr6:88117000-88117200	Enhancers	Brain Substantia Nigra	brain
25	chr6:88117000-88117200	Enhancers	Colon Smooth Muscle	Colon
26	chr6:88117000-88117200	Enhancers	Fetal Intestine Large	intestine
27	chr6:88117000-88117200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr6:88117000-88117200	Enhancers	Hela-S3	cervix
29	chr6:88117000-88117200	Flanking Active TSS	Osteobl	bone
30	chr6:88117000-88117400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:88117000-88117400	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr6:88117000-88117400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr6:88117000-88117400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr6:88117000-88117400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr6:88117000-88117400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:88117000-88117400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr6:88117000-88117400	Flanking Active TSS	Fetal Kidney	kidney
38	chr6:88117000-88117400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr6:88117000-88117400	Enhancers	Stomach Mucosa	stomach
40	chr6:88117000-88117400	Flanking Bivalent TSS/Enh	Dnd41	blood
41	chr6:88117000-88117400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
42	chr6:88117000-88117600	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr6:88117000-88117600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:88117000-88117600	Active TSS	Fetal Heart	heart
45	chr6:88117000-88117600	Flanking Active TSS	Fetal Intestine Small	intestine
46	chr6:88117000-88117600	Flanking Active TSS	HepG2	liver
47	chr6:88117000-88118400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:88117000-88118400	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr6:88117000-88118400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr6:88117000-88118400	Active TSS	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links