Variant report

Variant	rs12539172
Chromosome Location	chr7:100091795-100091796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:100090841..100092739-chr7:100123279..100124836,2	K562	blood:
2	chr7:100081775..100084583-chr7:100091175..100094124,2	MCF-7	breast:
3	chr7:100085482..100087607-chr7:100090109..100092006,2	K562	blood:
4	chr7:100083531..100085266-chr7:100090706..100092814,2	K562	blood:

Variant related genes	Relation type
ENSG00000166924	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1476679	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs2405442	1.00[ASW][hapmap];0.81[YRI][hapmap]
rs34919929	0.82[ASW][hapmap];0.81[CEU][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs34995835	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs6971558	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7778122	0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
2	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
3	nsv831071	chr7:99918025-100113413	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	287 gene(s)	inside rSNPs	diseases
4	nsv888776	chr7:100014711-100198386	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	297 gene(s)	inside rSNPs	diseases
5	nsv888777	chr7:100014711-100221867	Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
6	nsv888778	chr7:100014711-100236593	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	310 gene(s)	inside rSNPs	diseases
7	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
8	nsv888780	chr7:100032665-100198386	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
9	nsv527050	chr7:100056166-100125975	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv888781	chr7:100060928-100097895	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv888782	chr7:100064719-100236593	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
12	nsv888783	chr7:100073292-100136241	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	nsv888784	chr7:100076614-100097895	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12539172	FAM185A	cis	parietal	SCAN
rs12539172	GATS	cis	parietal	SCAN
rs12539172	PILRB	cis	Adipose Subcutaneous	GTEx
rs12539172	PVRIG2P	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100083600-100100800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr7:100085600-100098000	Weak transcription	Hela-S3	cervix
3	chr7:100088800-100104000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:100089200-100095600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr7:100089800-100091800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:100090000-100092800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:100090400-100092200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:100090800-100091800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr7:100090800-100091800	Bivalent/Poised TSS	HepG2	liver
10	chr7:100090800-100092000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
11	chr7:100090800-100092000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:100090800-100092000	Enhancers	Lung	lung
13	chr7:100090800-100092200	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
14	chr7:100091000-100091800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
15	chr7:100091000-100091800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
16	chr7:100091000-100091800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:100091000-100091800	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr7:100091000-100091800	Enhancers	Fetal Intestine Large	intestine
19	chr7:100091000-100091800	Enhancers	Placenta	Placenta
20	chr7:100091000-100091800	Enhancers	Pancreas	Pancrea
21	chr7:100091000-100091800	Active TSS	Rectal Smooth Muscle	rectum
22	chr7:100091000-100092000	Active TSS	H9 Cell Line	embryonic stem cell
23	chr7:100091000-100092000	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr7:100091000-100092000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr7:100091000-100092000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:100091000-100092000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr7:100091000-100092000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr7:100091000-100092000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr7:100091000-100092000	Enhancers	Liver	Liver
30	chr7:100091000-100092200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr7:100091000-100092200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr7:100091000-100092200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
33	chr7:100091000-100092200	Enhancers	Fetal Lung	lung
34	chr7:100091000-100092200	Bivalent Enhancer	Fetal Thymus	thymus
35	chr7:100091000-100092200	Enhancers	NHDF-Ad	bronchial
36	chr7:100091000-100092600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr7:100091200-100091800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr7:100091200-100091800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:100091200-100091800	Active TSS	Colon Smooth Muscle	Colon
40	chr7:100091200-100091800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
41	chr7:100091200-100091800	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr7:100091200-100091800	Transcr. at gene 5' and 3'	Right Atrium	heart
43	chr7:100091200-100092000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr7:100091200-100092000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
45	chr7:100091200-100092000	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr7:100091200-100092200	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr7:100091200-100092200	Enhancers	Fetal Brain Male	brain
48	chr7:100091200-100092200	Enhancers	Spleen	Spleen
49	chr7:100091200-100092400	Weak transcription	Brain Angular Gyrus	brain
50	chr7:100091400-100091800	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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