Variant report

Variant	rs722826
Chromosome Location	chr4:174098060-174098061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:174058621..174060538-chr4:174097948..174100109,2	K562	blood:
2	chr4:174091292..174097320-chr4:174098048..174101316,8	K562	blood:
3	chr4:174088223..174092682-chr4:174092972..174099857,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245213	Chromatin interaction
ENSG00000109586	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10005325	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10520255	1.00[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs10520256	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11942280	1.00[CEU][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs13102038	0.90[EUR][1000 genomes]
rs13116270	0.92[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13117810	0.95[EUR][1000 genomes]
rs13120215	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13123359	1.00[EUR][1000 genomes]
rs13123399	0.85[CEU][hapmap]
rs13124470	0.92[CEU][hapmap]
rs13141844	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs13142524	0.90[EUR][1000 genomes]
rs13150320	0.85[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs13151627	1.00[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs17059205	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs17059207	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs17059217	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17059235	0.85[CEU][hapmap]
rs1991726	0.85[CEU][hapmap]
rs2332657	0.86[EUR][1000 genomes]
rs2332658	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs28361970	0.91[EUR][1000 genomes]
rs28413646	0.87[EUR][1000 genomes]
rs28694391	0.83[EUR][1000 genomes]
rs34285915	0.81[EUR][1000 genomes]
rs34718403	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35576170	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35730812	0.83[EUR][1000 genomes]
rs35796775	0.82[EUR][1000 genomes]
rs36050097	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4608791	0.92[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs4695827	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4696050	0.86[EUR][1000 genomes]
rs4696054	0.92[CEU][hapmap]
rs62341096	0.92[EUR][1000 genomes]
rs6553686	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs6822924	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6835517	0.81[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs6858043	0.82[EUR][1000 genomes]
rs722827	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7661977	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7667345	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs7668473	0.91[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7669267	0.81[CEU][hapmap]
rs7673747	0.91[EUR][1000 genomes]
rs7689781	0.81[CEU][hapmap]
rs934358	0.85[GIH][hapmap]
rs9685410	0.85[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs9991863	0.86[EUR][1000 genomes]
rs9995556	0.92[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1793960	chr4:174090004-174102397	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv1801469	chr4:174090004-174102397	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1799519	chr4:174090004-174173743	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv1823585	chr4:174090209-174107537	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs722826	SCRG1	cis	parietal	SCAN
rs722826	GALNT7	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174091600-174113600	Weak transcription	Esophagus	oesophagus
2	chr4:174091800-174104000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr4:174092000-174098600	Weak transcription	Brain Angular Gyrus	brain
4	chr4:174092200-174098800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:174092200-174099000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr4:174092200-174099000	Enhancers	H9 Cell Line	embryonic stem cell
7	chr4:174092400-174100400	Weak transcription	Hela-S3	cervix
8	chr4:174092600-174099200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr4:174092600-174099200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr4:174092600-174102400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:174092800-174098600	Enhancers	Fetal Thymus	thymus
12	chr4:174092800-174099200	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr4:174092800-174099400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:174092800-174100400	Weak transcription	NHEK	skin
15	chr4:174092800-174101000	Weak transcription	HSMM	muscle
16	chr4:174092800-174103200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:174092800-174103600	Weak transcription	Aorta	Aorta
18	chr4:174092800-174106000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr4:174092800-174109000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:174093000-174102200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr4:174093600-174102400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:174093600-174109800	Weak transcription	Gastric	stomach
23	chr4:174093800-174105000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:174094200-174102800	Weak transcription	Brain Anterior Caudate	brain
25	chr4:174094600-174098600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:174095000-174109400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:174095200-174098800	Enhancers	Thymus	Thymus
28	chr4:174095400-174102800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:174095800-174102200	Weak transcription	Primary T cells from cord blood	blood
30	chr4:174096000-174100200	Weak transcription	HUVEC	blood vessel
31	chr4:174096200-174098400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr4:174096200-174100400	Weak transcription	Fetal Intestine Large	intestine
33	chr4:174096200-174100600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr4:174096200-174102000	Weak transcription	Fetal Intestine Small	intestine
35	chr4:174096200-174103200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:174096200-174111200	Weak transcription	Small Intestine	intestine
37	chr4:174096400-174101800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr4:174096600-174098800	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr4:174096800-174098200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr4:174096800-174098800	Weak transcription	Spleen	Spleen
41	chr4:174096800-174099200	Enhancers	K562	blood
42	chr4:174096800-174102000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr4:174096800-174103800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr4:174097000-174100400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:174097200-174098800	Enhancers	GM12878-XiMat	blood
46	chr4:174097200-174099000	Enhancers	Dnd41	blood
47	chr4:174097400-174098400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr4:174097400-174098600	Enhancers	A549	lung
49	chr4:174097400-174099000	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr4:174097600-174098400	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