Variant report

Variant	rs5762829
Chromosome Location	chr22:29228130-29228131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29227240..29229282-chr22:29232209..29234813,2	MCF-7	breast:
2	chr22:29227984..29230495-chr22:29230586..29232101,2	MCF-7	breast:
3	chr22:29226520..29228881-chr22:29235030..29237241,2	K562	blood:
4	chr22:29009654..29012223-chr22:29227592..29229292,2	K562	blood:
5	chr22:29221484..29225930-chr22:29227534..29231329,4	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10427628	0.86[EUR][1000 genomes]
rs12170231	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222	0.83[CEU][hapmap];0.86[TSI][hapmap]
rs13058031	0.83[CEU][hapmap];0.87[TSI][hapmap]
rs13058460	0.82[ASN][1000 genomes]
rs2267131	0.83[CEU][hapmap]
rs2301428	0.83[CEU][hapmap]
rs5752803	0.82[CEU][hapmap]
rs5752808	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752811	0.83[CEU][hapmap];0.87[TSI][hapmap]
rs5752814	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5752815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762764	0.86[YRI][hapmap]
rs5762814	0.83[CEU][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap]
rs5762816	0.83[CEU][hapmap];0.87[TSI][hapmap]
rs5762826	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762835	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762838	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762852	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5762855	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5762858	0.83[EUR][1000 genomes]
rs5762879	0.85[CEU][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap]
rs5997409	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997410	0.80[AMR][1000 genomes]
rs6005915	0.85[CEU][hapmap]
rs6005917	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625591	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625595	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625600	0.93[EUR][1000 genomes];0.89[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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs5762829	MN1	cis	cerebellum	SCAN
rs5762829	SUSD2	cis	parietal	SCAN
rs5762829	C22orf36	cis	cerebellum	SCAN
rs5762829	FLJ33814	cis	multi-tissue	Pritchard
rs5762829	XBP1	Cis_1M	lymphoblastoid	RTeQTL
rs5762829	RGL4	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29197200-29231600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr22:29198600-29231400	Weak transcription	HSMMtube	muscle
3	chr22:29198800-29230800	Weak transcription	NHEK	skin
4	chr22:29200600-29231400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr22:29214800-29242200	Weak transcription	Aorta	Aorta
6	chr22:29215600-29231600	Weak transcription	Right Ventricle	heart
7	chr22:29216000-29231600	Weak transcription	Placenta	Placenta
8	chr22:29216000-29232800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr22:29216000-29233800	Weak transcription	Left Ventricle	heart
10	chr22:29216000-29238600	Weak transcription	Spleen	Spleen
11	chr22:29218200-29231800	Weak transcription	Gastric	stomach
12	chr22:29219400-29234800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr22:29219600-29231800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr22:29224000-29237400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr22:29224200-29228200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr22:29225400-29242000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr22:29225800-29228800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr22:29225800-29229000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr22:29225800-29231600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr22:29225800-29231800	Weak transcription	HSMM	muscle
21	chr22:29225800-29233000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr22:29226000-29228200	Weak transcription	Brain Anterior Caudate	brain
23	chr22:29226000-29229000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr22:29226000-29229000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr22:29226000-29229200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr22:29226000-29229600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr22:29226000-29230000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr22:29226000-29231600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr22:29226000-29233000	Weak transcription	Dnd41	blood
30	chr22:29226000-29248800	Weak transcription	Primary T cells from cord blood	blood
31	chr22:29226200-29230000	Weak transcription	Fetal Thymus	thymus
32	chr22:29226200-29230200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr22:29226200-29234600	Weak transcription	Brain Substantia Nigra	brain
34	chr22:29226200-29234800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr22:29226200-29239600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr22:29226200-29242800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr22:29226400-29231600	Weak transcription	Pancreas	Pancrea
38	chr22:29226400-29231600	Weak transcription	Thymus	Thymus
39	chr22:29226600-29231800	Weak transcription	Fetal Intestine Large	intestine
40	chr22:29226600-29241800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr22:29226600-29242200	Weak transcription	Fetal Muscle Leg	muscle
42	chr22:29227600-29229400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr22:29227800-29229600	Weak transcription	Fetal Intestine Small	intestine
44	chr22:29227800-29230000	Weak transcription	Lung	lung
45	chr22:29227800-29230400	Strong transcription	Fetal Stomach	stomach
46	chr22:29227800-29235000	Weak transcription	Liver	Liver
47	chr22:29228000-29230000	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links