Variant report

Variant	rs11897786
Chromosome Location	chr2:97506872-97506873
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97492698..97495238-chr2:97505220..97508779,3	MCF-7	breast:
2	chr2:97506810..97509446-chr2:97509731..97511932,2	MCF-7	breast:
3	chr2:97506571..97510288-chr2:97534230..97537776,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168758	Chromatin interaction
ENSG00000168763	Chromatin interaction
ENSG00000163126	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10203346	0.85[EUR][1000 genomes]
rs10439526	0.87[EUR][1000 genomes]
rs12172	0.85[EUR][1000 genomes]
rs12846	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1317911	1.00[CEU][hapmap];0.93[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]
rs1320146	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs1320149	1.00[CEU][hapmap];0.93[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]
rs13419073	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17119598	0.87[CEU][hapmap]
rs2276654	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs55674661	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58147284	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59244622	0.85[EUR][1000 genomes]
rs62152794	0.83[AMR][1000 genomes]
rs62152795	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62152834	0.87[EUR][1000 genomes]
rs62152860	0.85[EUR][1000 genomes]
rs62152863	0.84[EUR][1000 genomes]
rs62152864	0.84[EUR][1000 genomes]
rs6576986	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs6576987	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs6576989	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6753987	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72811623	0.87[EUR][1000 genomes]
rs72811629	0.81[EUR][1000 genomes]
rs7594727	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608621	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9948	0.87[CEU][hapmap]
rs9973492	0.88[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
11	nsv1009720	chr2:97464803-97522856	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv535830	chr2:97464803-97522856	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11897786	FAHD2CP	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97484600-97518400	Weak transcription	HUVEC	blood vessel
2	chr2:97489400-97509000	Strong transcription	Brain Cingulate Gyrus	brain
3	chr2:97490200-97507800	Strong transcription	Brain Anterior Caudate	brain
4	chr2:97496200-97512400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:97498400-97513400	Weak transcription	NHEK	skin
6	chr2:97499200-97507400	Weak transcription	Psoas Muscle	Psoas
7	chr2:97499200-97507600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:97499200-97512400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:97499200-97512800	Weak transcription	Osteobl	bone
10	chr2:97499200-97513200	Weak transcription	Aorta	Aorta
11	chr2:97499200-97513400	Weak transcription	Small Intestine	intestine
12	chr2:97499200-97513600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:97499200-97522400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:97499400-97513200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr2:97499600-97513200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:97499600-97515600	Weak transcription	HSMMtube	muscle
17	chr2:97499600-97515800	Weak transcription	Fetal Kidney	kidney
18	chr2:97499600-97522800	Weak transcription	HSMM	muscle
19	chr2:97501000-97512000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:97501000-97512400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:97501000-97513000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:97501000-97520600	Weak transcription	Fetal Brain Male	brain
23	chr2:97501200-97515800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:97501200-97520600	Weak transcription	Hela-S3	cervix
25	chr2:97501800-97513200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:97502000-97513200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:97502600-97507000	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr2:97502600-97507000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:97503000-97507800	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr2:97503200-97514400	Strong transcription	Fetal Brain Female	brain
31	chr2:97503400-97507000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:97503400-97507000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:97503400-97507000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:97503400-97508400	Strong transcription	Brain Germinal Matrix	brain
35	chr2:97503600-97507000	Strong transcription	Placenta	Placenta
36	chr2:97503600-97522600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr2:97504000-97508400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:97504000-97512600	Weak transcription	A549	lung
39	chr2:97504000-97513400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr2:97504200-97509600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
41	chr2:97504200-97513400	Weak transcription	K562	blood
42	chr2:97504400-97507600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:97504400-97508000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
44	chr2:97504800-97508000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:97505000-97520400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:97505600-97507000	Strong transcription	Pancreas	Pancrea
47	chr2:97505600-97507600	Weak transcription	Right Atrium	heart
48	chr2:97505600-97511800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:97505600-97511800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:97505600-97512000	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links