Variant report

Variant	rs10874468
Chromosome Location	chr2:97595991-97595992
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:97549380..97552349-chr2:97593261..97597032,3	K562	blood:
2	chr2:97593138..97594730-chr2:97595667..97597186,2	K562	blood:
3	chr2:97587758..97596829-chr2:97597446..97601811,11	K562	blood:
4	chr2:97589310..97591841-chr2:97591978..97596020,4	MCF-7	breast:
5	chr2:97516728..97547486-chr2:97588377..97628331,265	MCF-7	breast:
6	chr2:97593591..97596299-chr2:97605457..97607301,3	K562	blood:
7	chr2:97557612..97562029-chr2:97591697..97596202,5	MCF-7	breast:
8	chr2:97595378..97599170-chr2:97599205..97602080,3	K562	blood:
9	chr2:97540516..97542905-chr2:97593439..97596324,2	K562	blood:
10	chr2:97592320..97594730-chr2:97595418..97597186,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000213337	Chromatin interaction
ENSG00000168754	Chromatin interaction
ENSG00000163126	Chromatin interaction
ENSG00000168758	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11164113	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11676858	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11680224	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1257021	0.81[CHB][hapmap]
rs1257022	0.87[MEX][hapmap]
rs1257026	0.91[ASW][hapmap]
rs12997297	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13009659	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1320147	0.83[ASW][hapmap]
rs13403225	0.83[ASW][hapmap]
rs1796043	0.97[GIH][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs7594227	0.83[ASW][hapmap]

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	nsv582497	chr2:97569305-97715154	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	nsv1001432	chr2:97591069-97671395	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10874468	CIAO1	cis	lymphoblastoid	seeQTL
rs10874468	FAHD2B	cis	cerebellum	SCAN
rs10874468	NEURL3	cis	parietal	SCAN
rs10874468	ZAP70	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97593600-97596800	Weak transcription	Brain Germinal Matrix	brain
2	chr2:97593600-97599400	Weak transcription	Gastric	stomach
3	chr2:97593800-97597800	Weak transcription	Pancreas	Pancrea
4	chr2:97593800-97599200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:97594000-97597800	Weak transcription	Right Atrium	heart
6	chr2:97594000-97610200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:97594200-97598400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:97594400-97596200	Weak transcription	Brain Substantia Nigra	brain
9	chr2:97594400-97596200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr2:97594400-97597000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:97594400-97597000	Weak transcription	Fetal Brain Female	brain
12	chr2:97594600-97596200	Weak transcription	Brain Angular Gyrus	brain
13	chr2:97594600-97596200	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:97594600-97596200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:97594600-97596200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:97594600-97596800	Weak transcription	Brain Anterior Caudate	brain
17	chr2:97594600-97597200	Weak transcription	HMEC	breast
18	chr2:97594600-97597800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:97595200-97596400	Enhancers	Esophagus	oesophagus
20	chr2:97595200-97597200	Weak transcription	Fetal Brain Male	brain
21	chr2:97595400-97596400	Enhancers	K562	blood
22	chr2:97595600-97596000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:97595600-97597200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:97595600-97597800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:97595800-97596200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links