Variant report

Variant	rs756202
Chromosome Location	chr6:37460350-37460351
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37458847..37461415-chr6:37462946..37464920,2	MCF-7	breast:
2	chr6:37454869..37462977-chr6:37463391..37469245,23	K562	blood:
3	chr6:37458120..37463201-chr6:37463391..37469475,12	K562	blood:

Variant related genes	Relation type
ENSG00000198937	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947673	0.83[CHB][hapmap]
rs11756941	0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12212090	0.90[ASN][1000 genomes]
rs1224127	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1224128	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1224129	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1812186	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252920	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2646926	0.86[ASN][1000 genomes]
rs2646933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2646934	0.84[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs2776873	0.81[EUR][1000 genomes]
rs2776881	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2776906	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2776908	0.92[ASN][1000 genomes]
rs2776910	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2776911	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2776916	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2797790	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4257849	0.85[ASN][1000 genomes]
rs62406516	0.96[ASN][1000 genomes]
rs904251	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs931649	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[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	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	esv3413317	chr6:37456674-37460972	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs756202	RP1-153P14.8	cis	Whole Blood	GTEx
rs756202	C6orf129	cis	parietal	SCAN
rs756202	RNF8	cis	cerebellum	SCAN
rs756202	C6orf129	cis	temporal cortex	BrainEAC
rs756202	RP1-153P14.5	cis	Whole Blood	GTEx
rs756202	FTSJD2	cis	parietal	SCAN
rs756202	C6orf129	cis	brain	BrainEAC

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37443600-37466600	Weak transcription	A549	lung
2	chr6:37446800-37466600	Weak transcription	Hela-S3	cervix
3	chr6:37447600-37466800	Weak transcription	HSMM	muscle
4	chr6:37448400-37466800	Weak transcription	Stomach Mucosa	stomach
5	chr6:37450200-37467200	Weak transcription	Small Intestine	intestine
6	chr6:37451400-37465600	Weak transcription	Colonic Mucosa	Colon
7	chr6:37451600-37466800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:37451600-37467000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:37451800-37462400	Enhancers	Fetal Brain Male	brain
10	chr6:37451800-37466600	Weak transcription	Primary B cells from cord blood	blood
11	chr6:37451800-37466800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:37452000-37460800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:37452000-37460800	Weak transcription	Ovary	ovary
14	chr6:37452000-37462200	Weak transcription	Aorta	Aorta
15	chr6:37452000-37466600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:37452000-37466800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:37452200-37466800	Weak transcription	NHLF	lung
18	chr6:37452600-37461000	Weak transcription	Gastric	stomach
19	chr6:37452600-37466800	Weak transcription	NHDF-Ad	bronchial
20	chr6:37452600-37466800	Weak transcription	Osteobl	bone
21	chr6:37453200-37466600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:37453400-37466800	Weak transcription	Fetal Intestine Large	intestine
23	chr6:37454200-37460400	Enhancers	Fetal Brain Female	brain
24	chr6:37454600-37464400	Weak transcription	K562	blood
25	chr6:37455000-37461000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:37455000-37461800	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr6:37455600-37460800	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr6:37455600-37461800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:37455600-37463800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr6:37455800-37460800	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr6:37456000-37460600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr6:37456200-37460600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr6:37456200-37464400	Enhancers	Primary T cells fromperipheralblood	blood
34	chr6:37456400-37461200	Enhancers	Fetal Thymus	thymus
35	chr6:37456400-37461800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:37456400-37467000	Weak transcription	Fetal Intestine Small	intestine
37	chr6:37456600-37460600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:37456600-37460800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr6:37456600-37466800	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr6:37456800-37460800	Weak transcription	Dnd41	blood
41	chr6:37457000-37460400	Enhancers	Right Ventricle	heart
42	chr6:37457000-37461000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr6:37457000-37461800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:37457200-37460600	Enhancers	Brain Cingulate Gyrus	brain
45	chr6:37457200-37460800	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr6:37457200-37461200	Enhancers	Fetal Muscle Trunk	muscle
47	chr6:37457200-37461400	Enhancers	Fetal Muscle Leg	muscle
48	chr6:37457200-37461600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:37457200-37461800	Enhancers	H1 Cell Line	embryonic stem cell
50	chr6:37457400-37460600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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