Variant report

Variant	rs1970162
Chromosome Location	chr9:71953719-71953720
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	chr9:71950254..71952717-chr9:71953240..71956144,4	MCF-7	breast:
2	chr9:71938069..71941613-chr9:71952585..71956255,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1334310	1.00[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7041728	0.82[LWK][hapmap];1.00[YRI][hapmap]

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	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1970162	FAM189A2	cis	parietal	SCAN
rs1970162	TJP2	cis	parietal	SCAN
rs1970162	SPPL3	trans	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71941400-71954400	Weak transcription	Brain Anterior Caudate	brain
2	chr9:71942800-71954400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr9:71943200-71954400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:71944600-71954400	Weak transcription	Brain Substantia Nigra	brain
5	chr9:71947000-71958000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr9:71947200-71954400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:71947200-71962000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:71947400-71954600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:71947600-71954400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:71948800-71962000	Weak transcription	Pancreas	Pancrea
11	chr9:71949400-71954400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr9:71949400-71954400	Weak transcription	HMEC	breast
13	chr9:71949600-71954600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:71950600-71954400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr9:71950600-71959400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:71950800-71954200	Weak transcription	Ovary	ovary
17	chr9:71950800-71954400	Weak transcription	Left Ventricle	heart
18	chr9:71950800-71954400	Weak transcription	Right Ventricle	heart
19	chr9:71950800-71959400	Weak transcription	Lung	lung
20	chr9:71951000-71954000	Weak transcription	Psoas Muscle	Psoas
21	chr9:71951000-71954200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr9:71951000-71954600	Weak transcription	Gastric	stomach
23	chr9:71951600-71955200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr9:71952200-71956200	Weak transcription	Fetal Muscle Leg	muscle
25	chr9:71952800-71955400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr9:71953600-71955400	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links