Variant report

Variant	rs6722670
Chromosome Location	chr2:172172864-172172865
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172163945..172166501-chr2:172172840..172175232,2	MCF-7	breast:
2	chr2:172172770..172175059-chr2:172182962..172185953,2	K562	blood:
3	chr2:172172855..172175323-chr2:172409152..172411417,2	K562	blood:
4	chr2:172172261..172175023-chr2:172288680..172291417,3	K562	blood:

Variant related genes	Relation type
ENSG00000123600	Chromatin interaction
ENSG00000115827	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10454741	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11674632	0.90[CEU][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11679835	0.90[CEU][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs11687454	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11691073	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12105780	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12989392	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12989938	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12995219	0.84[AMR][1000 genomes]
rs12998320	0.96[GIH][hapmap]
rs13000846	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13002817	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13002867	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13003130	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13005615	0.86[EUR][1000 genomes]
rs13023287	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13023973	0.92[GIH][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13031794	0.92[GIH][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13398989	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2111459	0.85[ASW][hapmap];0.92[GIH][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2356707	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34096402	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34787101	0.82[EUR][1000 genomes]
rs7592018	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6722670	STAT6	trans	brain	seeQTL
rs6722670	CDCA7	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172163800-172181400	Weak transcription	Gastric	stomach
2	chr2:172165600-172179400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:172167600-172174000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr2:172168800-172174800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:172169000-172174800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:172169200-172175000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:172169200-172175000	Weak transcription	Adipose Nuclei	Adipose
8	chr2:172169200-172175600	Weak transcription	HepG2	liver
9	chr2:172169200-172178800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:172169200-172182400	Weak transcription	Aorta	Aorta
11	chr2:172169200-172193400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:172169400-172173400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:172169400-172179400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:172169600-172175200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:172169600-172179400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:172169800-172177200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:172169800-172181200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:172169800-172183200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:172170200-172192800	Weak transcription	Fetal Intestine Large	intestine
20	chr2:172170400-172173200	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr2:172170600-172178000	Weak transcription	Dnd41	blood
22	chr2:172170800-172175600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr2:172170800-172177800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:172171000-172173200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr2:172171000-172173200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr2:172171000-172175200	Weak transcription	Primary T cells from cord blood	blood
27	chr2:172171000-172177400	Enhancers	H1 Cell Line	embryonic stem cell
28	chr2:172171200-172175000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr2:172171200-172175200	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr2:172171200-172175200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:172171200-172178000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:172171400-172190800	Weak transcription	Esophagus	oesophagus
33	chr2:172171600-172174000	Weak transcription	NHEK	skin
34	chr2:172171600-172176000	Weak transcription	K562	blood
35	chr2:172171800-172173400	Weak transcription	Primary B cells from peripheral blood	blood
36	chr2:172171800-172211600	Weak transcription	Fetal Intestine Small	intestine
37	chr2:172172000-172173600	Weak transcription	Brain Substantia Nigra	brain
38	chr2:172172000-172177600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr2:172172000-172177800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr2:172172200-172173400	Genic enhancers	GM12878-XiMat	blood
41	chr2:172172200-172173600	Enhancers	HUVEC	blood vessel
42	chr2:172172200-172175400	Enhancers	Fetal Muscle Leg	muscle
43	chr2:172172400-172173000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:172172400-172173000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr2:172172400-172173000	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr2:172172400-172173200	Enhancers	Brain Anterior Caudate	brain
47	chr2:172172400-172173200	Enhancers	Fetal Stomach	stomach
48	chr2:172172400-172173400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr2:172172400-172173600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:172172400-172173800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links