Variant report

Variant	rs7856021
Chromosome Location	chr9:93578499-93578500
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:93563428..93565399-chr9:93578384..93582187,4	MCF-7	breast:
2	chr9:93566333..93568000-chr9:93577767..93579301,2	MCF-7	breast:
3	chr9:93560904..93565448-chr9:93577288..93580605,5	K562	blood:
4	chr9:93569272..93571391-chr9:93577022..93579806,2	K562	blood:
5	chr9:93561901..93563996-chr9:93577117..93579715,2	MCF-7	breast:
6	chr9:93560904..93565448-chr9:93577148..93580132,4	K562	blood:

Variant related genes	Relation type
ENSG00000165025	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10993693	0.91[CHB][hapmap]
rs12350798	0.87[CHB][hapmap]
rs1319677	0.91[CHB][hapmap]
rs1333630	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333635	0.91[CHB][hapmap]
rs2562396	0.87[CHB][hapmap]
rs2780701	0.87[CHB][hapmap]
rs290985	0.99[ASN][1000 genomes]
rs290990	0.83[CHB][hapmap]
rs290991	0.83[CHB][hapmap]
rs4744505	0.82[LWK][hapmap]
rs914925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7856021	ISCA1	cis	parietal	SCAN
rs7856021	CENPP	cis	cerebellum	SCAN

Chromatin state (count:44 , 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	chr9:93567800-93584800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:93567800-93584800	Weak transcription	Fetal Intestine Large	intestine
4	chr9:93567800-93597400	Weak transcription	Gastric	stomach
5	chr9:93572600-93591000	Weak transcription	Lung	lung
6	chr9:93572800-93584800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr9:93573200-93589600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:93574600-93578600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:93574600-93578800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr9:93574800-93580200	Weak transcription	Pancreas	Pancrea
11	chr9:93575000-93580600	Weak transcription	Stomach Mucosa	stomach
12	chr9:93575200-93580400	Weak transcription	Fetal Intestine Small	intestine
13	chr9:93576200-93579000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr9:93576400-93580200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr9:93576600-93578800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:93576800-93578600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr9:93576800-93582400	Weak transcription	Small Intestine	intestine
18	chr9:93577000-93578600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr9:93577000-93585800	Genic enhancers	Primary B cells from peripheral blood	blood
20	chr9:93577000-93598800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:93577200-93578600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:93577200-93589000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr9:93577600-93578600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
24	chr9:93577600-93578600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
25	chr9:93577600-93578600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
26	chr9:93577600-93578800	Enhancers	Fetal Kidney	kidney
27	chr9:93577800-93582200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr9:93577800-93584000	Weak transcription	HMEC	breast
29	chr9:93577800-93584800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr9:93577800-93585000	Weak transcription	Spleen	Spleen
31	chr9:93577800-93606200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:93578000-93578800	Enhancers	Dnd41	blood
33	chr9:93578000-93585000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:93578200-93578800	Enhancers	Fetal Thymus	thymus
35	chr9:93578200-93578800	Enhancers	Thymus	Thymus
36	chr9:93578200-93582400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:93578200-93585000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr9:93578400-93578600	Enhancers	Esophagus	oesophagus
39	chr9:93578400-93578800	Enhancers	Primary B cells from cord blood	blood
40	chr9:93578400-93578800	Enhancers	GM12878-XiMat	blood
41	chr9:93578400-93578800	Enhancers	K562	blood
42	chr9:93578400-93579000	Enhancers	Primary hematopoietic stem cells	blood
43	chr9:93578400-93579400	Genic enhancers	Monocytes-CD14+_RO01746	blood
44	chr9:93578400-93580400	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links