Variant report

Variant	rs929454
Chromosome Location	chr22:30692353-30692354
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30691985..30694269-chr22:30820626..30822582,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242114	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10376	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427610	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1043099	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1046199	0.80[CHD][hapmap]
rs2041199	0.89[AMR][1000 genomes]
rs2108093	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[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299830	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4339043	1.00[ASW][hapmap];0.95[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820831	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[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4820844	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4823085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749066	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749082	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5753071	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753080	1.00[ASW][hapmap];0.95[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753088	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753111	1.00[ASN][1000 genomes]
rs5763923	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap]
rs737950	1.00[ASW][hapmap];0.95[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs740219	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[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757869	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs9608904	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9619104	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914968	chr22:30610570-30693581	Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv914972	chr22:30640308-30693581	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1062388	chr22:30649179-30711443	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	esv1799458	chr22:30659798-30698035	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs929454	SF3A1	cis	multi-tissue	Pritchard
rs929454	SELM	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30686000-30700000	Weak transcription	Fetal Kidney	kidney
2	chr22:30686200-30720000	Weak transcription	Fetal Brain Male	brain
3	chr22:30686400-30701800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr22:30686600-30700600	Genic enhancers	Fetal Thymus	thymus
5	chr22:30686800-30694800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr22:30686800-30701800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr22:30686800-30707200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr22:30687000-30695800	Strong transcription	Brain Germinal Matrix	brain
9	chr22:30687000-30699600	Strong transcription	Fetal Brain Female	brain
10	chr22:30687200-30697200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr22:30687400-30695200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr22:30687400-30695800	Strong transcription	Primary B cells from cord blood	blood
13	chr22:30687400-30696400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr22:30687400-30696600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr22:30687400-30701200	Weak transcription	K562	blood
16	chr22:30687400-30706800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr22:30687600-30693000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr22:30687600-30693400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr22:30687600-30694000	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr22:30687600-30694200	Strong transcription	Fetal Intestine Large	intestine
21	chr22:30687600-30694600	Strong transcription	Fetal Intestine Small	intestine
22	chr22:30687600-30695600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr22:30687600-30696400	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr22:30687600-30697200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr22:30687600-30699000	Weak transcription	HepG2	liver
26	chr22:30687600-30699800	Genic enhancers	Esophagus	oesophagus
27	chr22:30687600-30701400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr22:30687800-30693600	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr22:30687800-30694200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr22:30687800-30696400	Weak transcription	NHDF-Ad	bronchial
31	chr22:30687800-30696600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr22:30687800-30697600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr22:30687800-30698000	Strong transcription	Osteobl	bone
34	chr22:30688000-30693600	Strong transcription	Colon Smooth Muscle	Colon
35	chr22:30688000-30694000	Strong transcription	Colonic Mucosa	Colon
36	chr22:30688000-30694000	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr22:30688000-30694200	Strong transcription	Rectal Smooth Muscle	rectum
38	chr22:30688000-30694400	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr22:30688000-30697400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr22:30688000-30697400	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr22:30688000-30697600	Weak transcription	HUVEC	blood vessel
42	chr22:30688200-30692400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr22:30688200-30692600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr22:30688200-30693400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr22:30688200-30693600	Strong transcription	Fetal Lung	lung
46	chr22:30688200-30694000	Strong transcription	Dnd41	blood
47	chr22:30688200-30696400	Strong transcription	Adipose Nuclei	Adipose
48	chr22:30688200-30696800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr22:30688200-30697200	Weak transcription	Brain Angular Gyrus	brain
50	chr22:30688200-30697200	Strong transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links