Variant report

Variant	rs290238
Chromosome Location	chr9:93574494-93574495
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:93561656..93565893-chr9:93566155..93575937,12	MCF-7	breast:
2	chr9:93573891..93575434-chr9:93575492..93578203,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165025	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12550873	0.83[ASW][hapmap]
rs158508	1.00[CHB][hapmap]
rs1755958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1760124	1.00[CHB][hapmap]
rs2035072	1.00[CHB][hapmap]
rs2613310	1.00[CHB][hapmap]
rs2613320	1.00[CHB][hapmap]
rs290213	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs290225	1.00[CHB][hapmap]
rs290232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290234	1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290236	1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290237	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][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];1.00[ASN][1000 genomes]
rs290256	1.00[CHB][hapmap]
rs60044325	0.80[AFR][1000 genomes]
rs965892	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv893567	chr9:93519280-93609668	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv831652	chr9:93527411-93696923	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv893569	chr9:93552550-93587089	Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1038685	chr9:93556174-93685729	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs290238	ISCA1	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93565000-93609000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr9:93565400-93577000	Weak transcription	Colonic Mucosa	Colon
3	chr9:93567800-93584800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:93567800-93584800	Weak transcription	Fetal Intestine Large	intestine
5	chr9:93567800-93597400	Weak transcription	Gastric	stomach
6	chr9:93568400-93575000	Enhancers	Fetal Thymus	thymus
7	chr9:93568400-93576600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr9:93569600-93574600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:93571000-93575200	Strong transcription	Fetal Intestine Small	intestine
10	chr9:93571200-93576200	Genic enhancers	Primary monocytes fromperipheralblood	blood
11	chr9:93571200-93576600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:93571400-93576600	Weak transcription	Small Intestine	intestine
13	chr9:93571400-93576800	Weak transcription	Primary T cells from cord blood	blood
14	chr9:93571600-93575800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr9:93571800-93577600	Weak transcription	Fetal Kidney	kidney
16	chr9:93572000-93576000	Genic enhancers	Monocytes-CD14+_RO01746	blood
17	chr9:93572400-93575000	Enhancers	Stomach Mucosa	stomach
18	chr9:93572600-93575400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr9:93572600-93591000	Weak transcription	Lung	lung
20	chr9:93572800-93574600	Weak transcription	Spleen	Spleen
21	chr9:93572800-93576800	Weak transcription	Esophagus	oesophagus
22	chr9:93572800-93584800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr9:93573000-93575400	Weak transcription	Fetal Stomach	stomach
24	chr9:93573200-93575800	Weak transcription	K562	blood
25	chr9:93573200-93576600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:93573200-93589600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr9:93573400-93577200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:93573600-93577000	Enhancers	Primary B cells from peripheral blood	blood
29	chr9:93574000-93574600	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr9:93574000-93574600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr9:93574000-93574800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:93574000-93577400	Enhancers	Primary hematopoietic stem cells	blood
33	chr9:93574200-93574600	Weak transcription	Pancreas	Pancrea
34	chr9:93574200-93577000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:93574200-93577600	Weak transcription	HMEC	breast
36	chr9:93574400-93574600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:93574400-93574800	Flanking Active TSS	GM12878-XiMat	blood
38	chr9:93574400-93575000	Genic enhancers	Thymus	Thymus
39	chr9:93574400-93575400	Genic enhancers	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links