Variant report

Variant	rs11676858
Chromosome Location	chr2:97597577-97597578
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:97596756..97599401-chr2:97603450..97605798,2	K562	blood:
2	chr2:97516728..97547486-chr2:97588377..97628331,265	MCF-7	breast:
3	chr2:97582821..97585259-chr2:97596994..97599468,2	K562	blood:
4	chr2:97597541..97599425-chr2:97607276..97609222,2	MCF-7	breast:
5	chr2:97595378..97599170-chr2:97599205..97602080,3	K562	blood:
6	chr2:97587758..97596829-chr2:97597446..97601811,11	K562	blood:
7	chr2:97591472..97593317-chr2:97596171..97598868,2	MCF-7	breast:
8	chr2:97596397..97598597-chr2:97601804..97605684,3	MCF-7	breast:
9	chr2:97534503..97536354-chr2:97596244..97598088,2	K562	blood:

No data

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

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10874468	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]
rs11164113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11680224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11688134	0.83[AMR][1000 genomes]
rs1257021	0.88[CHB][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs1257022	1.00[ASW][hapmap];0.84[CHD][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs1257026	0.85[CHB][hapmap];0.86[MKK][hapmap]
rs1257084	1.00[ASW][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[YRI][hapmap]
rs1257089	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap]
rs1257101	0.81[CHB][hapmap]
rs1257117	0.85[CHB][hapmap];1.00[YRI][hapmap]
rs12997297	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13009659	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1669760	0.82[CHB][hapmap]
rs1796043	1.00[ASW][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap];0.86[AMR][1000 genomes]
rs2463904	0.85[CHB][hapmap];1.00[YRI][hapmap]
rs7569432	0.81[CHB][hapmap]
rs9324210	0.81[AMR][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	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
rs11676858	ANKRD36B	cis	Thyroid	GTEx
rs11676858	CIAO1	cis	lymphoblastoid	seeQTL
rs11676858	ZAP70	cis	cerebellum	SCAN
rs11676858	FAHD2B	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97593600-97599400	Weak transcription	Gastric	stomach
2	chr2:97593800-97597800	Weak transcription	Pancreas	Pancrea
3	chr2:97593800-97599200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:97594000-97597800	Weak transcription	Right Atrium	heart
5	chr2:97594000-97610200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:97594200-97598400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:97594600-97597800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:97595600-97597800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:97596000-97598200	Enhancers	Brain Cingulate Gyrus	brain
10	chr2:97596200-97597600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:97596200-97598200	Enhancers	Brain Angular Gyrus	brain
12	chr2:97596200-97598400	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr2:97596400-97597800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:97596400-97597800	Weak transcription	Esophagus	oesophagus
15	chr2:97596800-97597600	Enhancers	Brain Anterior Caudate	brain
16	chr2:97596800-97597800	Bivalent Enhancer	NHEK	skin
17	chr2:97596800-97598000	Enhancers	Brain Hippocampus Middle	brain
18	chr2:97596800-97598000	Enhancers	Brain Substantia Nigra	brain
19	chr2:97596800-97598200	Enhancers	Brain Germinal Matrix	brain
20	chr2:97596800-97598400	Bivalent Enhancer	Fetal Muscle Leg	muscle
21	chr2:97597000-97597600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:97597000-97597600	Enhancers	Fetal Brain Female	brain
23	chr2:97597000-97597800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:97597000-97598000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr2:97597000-97598000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:97597200-97597800	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr2:97597200-97598000	Enhancers	Fetal Brain Male	brain
28	chr2:97597200-97598200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr2:97597200-97598200	Enhancers	HMEC	breast
30	chr2:97597200-97606000	Weak transcription	Fetal Thymus	thymus
31	chr2:97597400-97597800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:97597400-97597800	Enhancers	K562	blood

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