Variant report

Variant	rs7749047
Chromosome Location	chr6:88106593-88106594
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:88106277-88106708	H1-neurons	neurons:	n/a	n/a
2	SPI1	chr6:88106385-88107194	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:88106366-88106622	H1-neurons	neurons:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:88106569-88106619	BE2_C	brain:	n/a
2	chr6:88106569-88106619	ovcar-3	ovarian:	n/a
3	chr6:88106569-88106619	AG04449	skin:	fetal
4	chr6:88106569-88106619	MCF-7	breast:	n/a
5	chr6:88106569-88106619	SKMC	muscle:	n/a
6	chr6:88106569-88106619	GM19239	blood:	n/a
7	chr6:88106569-88106619	BJ	skin:	n/a
8	chr6:88106569-88106619	NB4	blood:	n/a
9	chr6:88106569-88106619	AoSMC	blood vessel:	n/a
10	chr6:88106569-88106619	HPAEpiC	pulmonary alveolar:	n/a
11	chr6:88106569-88106619	T-47D	breast:	n/a
12	chr6:88106569-88106619	GM06990	blood:	n/a
13	chr6:88106569-88106619	CMK	blood:	n/a
14	chr6:88106569-88106619	HRPEpiC	eye:	n/a
15	chr6:88106569-88106619	GM12892	blood:	n/a
16	chr6:88106569-88106619	PANC-1	pancreas:	n/a
17	chr6:88106569-88106619	HL-60	blood:	n/a
18	chr6:88106569-88106619	HRE	kidney:	n/a
19	chr6:88106569-88106619	HUVEC	blood vessel:	n/a
20	chr6:88106569-88106619	NHBE	bronchial:	n/a
21	chr6:88106569-88106619	NT2-D1	testis:	n/a
22	chr6:88106569-88106619	PFSK-1	brain:	n/a
23	chr6:88106569-88106619	HCPEpiC	choroid plexus:	n/a
24	chr6:88106569-88106619	H1-hESC	embryonic stem cell:	embryo
25	chr6:88106569-88106619	Caco-2	colon:	n/a
26	chr6:88106569-88106619	SAEC	small airway:	n/a
27	chr6:88106569-88106619	SK-N-SH_RA	brain:	n/a
28	chr6:88106569-88106619	HIPEpiC	eye:	n/a
29	chr6:88106569-88106619	HCT-116	colon:	n/a
30	chr6:88106569-88106619	NH-A	brain:	n/a
31	chr6:88106569-88106619	LNCaP	prostate:	n/a
32	chr6:88106569-88106619	GM12891	blood:	n/a
33	chr6:88106569-88106619	U87	brain:	n/a
34	chr6:88106569-88106619	K562	blood:	n/a
35	chr6:88106569-88106619	HEK293	kidney:	embryo
36	chr6:88106569-88106619	AG04450	lung:	fetal
37	chr6:88106569-88106619	MCF10A-Er-Src	breast:	n/a
38	chr6:88106569-88106619	ECC-1	luminal epithelium:	n/a
39	chr6:88106569-88106619	RPTEC	kidney:	n/a
40	chr6:88106569-88106619	HRCEpiC	kidney:	n/a
41	chr6:88106569-88106619	HAEpiC	amniotic membrane:	n/a
42	chr6:88106569-88106619	SK-N-SH	brain:	n/a
43	chr6:88106569-88106619	Hela-S3	cervix:	n/a
44	chr6:88106569-88106619	IMR90	lung:	fetal
45	chr6:88106569-88106619	HCF	heart:	n/a
46	chr6:88106569-88106619	GM12878	blood:	n/a
47	chr6:88106569-88106619	AG10803	skin:	n/a
48	chr6:88106569-88106619	A549	lung:	n/a
49	chr6:88106569-88106619	NHDF-neo	bronchial:	n/a
50	chr6:88106569-88106619	HEEpiC	esophagus:	n/a

No data

Variant related genes	Relation type
C6orf164	TF binding region
C6orf164	CpG island

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

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1051550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964198	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11964212	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11964237	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11966859	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203156	1.00[JPT][hapmap]
rs12529410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12529423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12661245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12663865	0.85[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13211410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13211836	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13217485	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs242291	1.00[JPT][hapmap]
rs34977536	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35332886	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35869302	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3736740	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]
rs4329082	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4707365	0.86[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4707367	0.85[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4707368	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4707369	0.90[ASN][1000 genomes]
rs4707370	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707372	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5009694	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6454610	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6454611	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6454612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6454613	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6454614	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6454615	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6454616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs6454617	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6454618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs6454621	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6454622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6454623	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6454624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6454625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs6454626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs6899561	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6900397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6906433	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6907825	0.85[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6909168	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6910429	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6912282	0.93[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6912300	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6912442	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6912875	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6915562	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs6919775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6920937	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6930072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6940716	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs71541172	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7744338	0.85[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7744793	0.86[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7746469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7749162	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7753821	0.86[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7760108	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7761462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764266	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7764963	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs7766462	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7767220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773262	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7773804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs926946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9294378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9342112	0.83[ASN][1000 genomes]
rs9344708	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9344709	0.80[EUR][1000 genomes]
rs9353484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9353485	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9353486	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9353487	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9353488	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9362428	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9444493	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9444494	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9444495	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9444496	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450672	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs9450674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450682	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7749047	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs7749047	C6orf164	cis	lung	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88040600-88116800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:88054800-88110200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:88103200-88110600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:88103400-88109800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:88104400-88110200	Weak transcription	Pancreas	Pancrea
6	chr6:88106400-88117200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:88106400-88117200	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links