Variant report

Variant	rs7955798
Chromosome Location	chr12:8188963-8188964
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:8188281..8192732-chr12:8193522..8196171,4	K562	blood:
2	chr12:8188270..8191045-chr12:8232664..8235322,4	MCF-7	breast:
3	chr12:7281358..7283966-chr12:8188760..8190703,2	K562	blood:

Variant related genes	Relation type
ENSG00000139194	Chromatin interaction
ENSG00000256967	Chromatin interaction
ENSG00000139182	Chromatin interaction
ENSG00000089818	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10846377	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs17801353	0.87[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34994807	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3782681	0.94[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61922169	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs722458	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048545	chr12:7778760-8608231	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv541368	chr12:7778760-8608231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	esv1795892	chr12:7856819-8508693	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2758292	chr12:7856819-8623987	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	esv2759877	chr12:7856819-8623987	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv428270	chr12:7856819-8623987	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription 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	93 gene(s)	inside rSNPs	diseases
7	esv1797934	chr12:7985460-8214261	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
8	esv1793572	chr12:7995827-8568422	Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	nsv1040972	chr12:8003413-8266291	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
10	nsv541388	chr12:8003413-8266291	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
11	nsv916941	chr12:8003501-8608220	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers 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	86 gene(s)	inside rSNPs	diseases
12	esv2751118	chr12:8017473-8190206	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
13	nsv898729	chr12:8044997-8190206	Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
14	nsv1045521	chr12:8123225-8242846	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
15	nsv898732	chr12:8123306-8190206	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
16	nsv1040958	chr12:8177050-8309724	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
17	nsv541396	chr12:8177050-8309724	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7955798	PEX5	cis	parietal	SCAN
rs7955798	RPL13P5	cis	cerebellum	SCAN
rs7955798	CLEC4A	cis	parietal	SCAN
rs7955798	LAG3	cis	parietal	SCAN
rs7955798	C3AR1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8184600-8189000	Active TSS	Aorta	Aorta
2	chr12:8185800-8189400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr12:8186200-8189200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr12:8186200-8189400	Flanking Active TSS	Fetal Heart	heart
5	chr12:8186200-8191400	Enhancers	Small Intestine	intestine
6	chr12:8186400-8191000	Enhancers	Spleen	Spleen
7	chr12:8186600-8189200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr12:8186600-8191800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:8186600-8192800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:8186800-8189000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr12:8186800-8191000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr12:8186800-8191200	Enhancers	Fetal Thymus	thymus
13	chr12:8186800-8191800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr12:8186800-8191800	Enhancers	Lung	lung
15	chr12:8186800-8192200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:8187000-8189000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr12:8187000-8189200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:8187000-8189800	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr12:8187000-8190400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr12:8187000-8190600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:8187000-8191000	Enhancers	H9 Cell Line	embryonic stem cell
22	chr12:8187000-8191000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:8187000-8191200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr12:8187000-8191200	Enhancers	Pancreas	Pancrea
25	chr12:8187000-8192000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:8187200-8189200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr12:8187200-8189600	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr12:8187200-8189800	Genic enhancers	Fetal Muscle Trunk	muscle
29	chr12:8187200-8191200	Enhancers	Primary T cells fromperipheralblood	blood
30	chr12:8187200-8192000	Enhancers	Primary B cells from peripheral blood	blood
31	chr12:8187200-8192000	Enhancers	Liver	Liver
32	chr12:8187400-8189400	Enhancers	HUVEC	blood vessel
33	chr12:8187400-8191000	Weak transcription	A549	lung
34	chr12:8187600-8189000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr12:8187600-8189200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr12:8187600-8189200	Enhancers	Brain Cingulate Gyrus	brain
37	chr12:8187600-8190000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:8187600-8190600	Enhancers	Thymus	Thymus
39	chr12:8187600-8190800	Enhancers	HMEC	breast
40	chr12:8187600-8191000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:8187600-8191200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:8187600-8191200	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr12:8187600-8191200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:8187600-8192600	Genic enhancers	Fetal Muscle Leg	muscle
45	chr12:8187800-8189800	Enhancers	Primary hematopoietic stem cells	blood
46	chr12:8187800-8190600	Weak transcription	HSMM	muscle
47	chr12:8187800-8190800	Enhancers	Primary T cells from cord blood	blood
48	chr12:8187800-8190800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr12:8187800-8191000	Enhancers	Fetal Brain Female	brain
50	chr12:8187800-8191200	Enhancers	Fetal Lung	lung

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