Variant report

Variant	rs172164
Chromosome Location	chr6:28046478-28046479
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28046448-28046498	HUVEC	blood vessel:	n/a
2	chr6:28046448-28046498	Hela-S3	cervix:	n/a
3	chr6:28046448-28046498	HRCEpiC	kidney:	n/a
4	chr6:28046448-28046498	Hepatocyte	liver:	n/a
5	chr6:28046448-28046498	HAEpiC	amniotic membrane:	n/a
6	chr6:28046448-28046498	GM12892	blood:	n/a
7	chr6:28046448-28046498	NH-A	brain:	n/a
8	chr6:28046448-28046498	HRPEpiC	eye:	n/a
9	chr6:28046448-28046498	RPTEC	kidney:	n/a
10	chr6:28046448-28046498	HCPEpiC	choroid plexus:	n/a
11	chr6:28046448-28046498	HL-60	blood:	n/a
12	chr6:28046448-28046498	SK-N-SH_RA	brain:	n/a
13	chr6:28046448-28046498	HIPEpiC	eye:	n/a
14	chr6:28046448-28046498	AG09319	gingival:	n/a
15	chr6:28046448-28046498	SKMC	muscle:	n/a
16	chr6:28046448-28046498	HCF	heart:	n/a
17	chr6:28046448-28046498	HMEC	breast:	n/a
18	chr6:28046448-28046498	HEEpiC	esophagus:	n/a
19	chr6:28046448-28046498	ECC-1	luminal epithelium:	n/a
20	chr6:28046448-28046498	HepG2	liver:	n/a
21	chr6:28046448-28046498	AG09309	skin:	n/a
22	chr6:28046448-28046498	HNPCEpiC	eye:	n/a
23	chr6:28046448-28046498	Caco-2	colon:	n/a
24	chr6:28046448-28046498	NT2-D1	testis:	n/a
25	chr6:28046448-28046498	AoSMC	blood vessel:	n/a
26	chr6:28046448-28046498	BJ	skin:	n/a
27	chr6:28046448-28046498	LNCaP	prostate:	n/a
28	chr6:28046448-28046498	GM19239	blood:	n/a
29	chr6:28046448-28046498	MCF10A-Er-Src	breast:	n/a
30	chr6:28046448-28046498	NHDF-neo	bronchial:	n/a
31	chr6:28046448-28046498	HCT-116	colon:	n/a
32	chr6:28046448-28046498	HCM	heart:	n/a
33	chr6:28046448-28046498	GM06990	blood:	n/a
34	chr6:28046448-28046498	HEK293	kidney:	embryo
35	chr6:28046448-28046498	SK-N-MC	brain:	n/a
36	chr6:28046448-28046498	HRE	kidney:	n/a
37	chr6:28046448-28046498	IMR90	lung:	fetal
38	chr6:28046448-28046498	PANC-1	pancreas:	n/a
39	chr6:28046448-28046498	K562	blood:	n/a
40	chr6:28046448-28046498	ProgFib	skin:	n/a
41	chr6:28046448-28046498	U87	brain:	n/a
42	chr6:28046448-28046498	AG04449	skin:	fetal
43	chr6:28046448-28046498	NHBE	bronchial:	n/a
44	chr6:28046448-28046498	GM12878	blood:	n/a
45	chr6:28046448-28046498	ovcar-3	ovarian:	n/a
46	chr6:28046448-28046498	AG04450	lung:	fetal
47	chr6:28046448-28046498	A549	lung:	n/a
48	chr6:28046448-28046498	NB4	blood:	n/a
49	chr6:28046448-28046498	MCF-7	breast:	n/a
50	chr6:28046448-28046498	PrEC	prostate:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28046111..28048022-chr6:28095723..28098620,2	K562	blood:
2	chr6:28044681..28046793-chr6:28367579..28369114,2	K562	blood:
3	chr6:28045344..28046935-chr6:28047195..28048919,2	K562	blood:
4	chr6:28044713..28049958-chr6:28107484..28111355,5	K562	blood:
5	chr6:27864591..27866445-chr6:28044322..28046847,2	K562	blood:

No data

Variant related genes	Relation type
ZNF165	CpG island
ENSG00000197279	Chromatin interaction
ENSG00000238610	Chromatin interaction
ENSG00000272009	Chromatin interaction
ENSG00000198315	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1150672	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1150674	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1150676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1150680	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1150683	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1150684	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1225593	0.92[YRI][hapmap]
rs1225594	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1225709	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1225711	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233784	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1237873	1.00[ASW][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes]
rs1416997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1480646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs149898	0.85[YRI][hapmap]
rs149957	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1529749	1.00[CEU][hapmap]
rs156741	1.00[ASW][hapmap]
rs156742	1.00[ASW][hapmap]
rs1613149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1619221	0.92[YRI][hapmap]
rs1654777	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654778	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs169432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs169433	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs175955	0.92[YRI][hapmap]
rs1770130	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770132	1.00[YRI][hapmap]
rs1770133	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17709097	1.00[CEU][hapmap];0.94[GIH][hapmap]
rs17709109	1.00[CEU][hapmap]
rs17709523	1.00[CEU][hapmap]
rs17765491	1.00[CEU][hapmap]
rs1871695	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs200970	1.00[ASW][hapmap]
rs203865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203868	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203871	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203874	1.00[YRI][hapmap]
rs203875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203881	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203885	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203891	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394044	1.00[CEU][hapmap]
rs2622318	0.92[YRI][hapmap]
rs2622321	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs276364	1.00[ASW][hapmap]
rs2791334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs370266	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392665	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41375446	1.00[CEU][hapmap];0.94[GIH][hapmap]
rs425159	0.85[YRI][hapmap]
rs427348	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs539474	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57349346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58909320	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73740569	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73740570	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73742609	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348782	1.00[CEU][hapmap]
rs9348790	1.00[CEU][hapmap]
rs9348791	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348795	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357055	1.00[CEU][hapmap]
rs9357056	1.00[CEU][hapmap]
rs9366714	0.88[ASN][1000 genomes]
rs9368545	1.00[CEU][hapmap]
rs9368562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9380042	1.00[CEU][hapmap]
rs9393873	1.00[CEU][hapmap]
rs9393874	1.00[CEU][hapmap]
rs9393879	1.00[CEU][hapmap];0.94[GIH][hapmap]
rs9393905	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[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	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	esv33436	chr6:28044346-28049043	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs172164	ZNF165	cis	lymphoblastoid	seeQTL
rs172164	HIST1H3H	cis	lymphoblastoid	seeQTL
rs172164	Hs.158943	cis	multi-tissue	Pritchard
rs172164	ZNF165	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28042600-28046600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:28043200-28047800	Weak transcription	Spleen	Spleen
3	chr6:28045200-28047600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:28045600-28047800	Weak transcription	Right Atrium	heart
5	chr6:28045800-28047800	Weak transcription	Fetal Brain Male	brain
6	chr6:28046000-28047800	Weak transcription	Fetal Heart	heart
7	chr6:28046200-28047000	Enhancers	GM12878-XiMat	blood
8	chr6:28046200-28047400	Enhancers	K562	blood
9	chr6:28046400-28047600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links