Variant report

Variant	rs202147
Chromosome Location	chr7:101650302-101650303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:101582848..101590446-chr7:101646237..101653992,20	MCF-7	breast:
2	chr7:101343400..101345941-chr7:101650258..101652233,2	MCF-7	breast:
3	chr7:101616748..101619051-chr7:101648176..101650309,2	MCF-7	breast:
4	chr7:101457163..101465176-chr7:101645974..101654631,24	MCF-7	breast:
5	chr7:101610580..101623329-chr7:101643563..101654055,32	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10231075	1.00[JPT][hapmap]
rs10236615	1.00[JPT][hapmap]
rs10259603	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10276057	1.00[JPT][hapmap]
rs10488042	1.00[JPT][hapmap]
rs10488043	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12534969	1.00[CHD][hapmap]
rs12537526	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12668959	1.00[CHD][hapmap]
rs12672026	1.00[CHD][hapmap]
rs17408612	1.00[JPT][hapmap]
rs17408640	1.00[JPT][hapmap]
rs17487076	1.00[JPT][hapmap]
rs17487672	1.00[JPT][hapmap]
rs202142	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs202144	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs202145	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs202149	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202152	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202155	1.00[CHB][hapmap]
rs202158	1.00[CHB][hapmap]
rs202159	1.00[CHB][hapmap]
rs202164	0.95[ASN][1000 genomes]
rs2031085	1.00[JPT][hapmap]
rs4727515	1.00[CHB][hapmap]
rs4727516	1.00[CHB][hapmap]
rs4729768	1.00[CHB][hapmap]
rs6465839	1.00[JPT][hapmap]
rs6465845	1.00[CHB][hapmap]
rs6973312	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7780631	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7785266	1.00[JPT][hapmap]
rs7796818	1.00[JPT][hapmap]
rs7796995	1.00[JPT][hapmap]
rs7797764	1.00[CHD][hapmap]
rs7799576	1.00[CHB][hapmap]
rs7799663	1.00[CHD][hapmap]
rs7805379	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7809629	1.00[CHB][hapmap]
rs7810922	1.00[JPT][hapmap]
rs9969318	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv482846	chr7:101539981-101707666	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv888827	chr7:101562674-101650302	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv482521	chr7:101604002-101718950	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv831080	chr7:101629121-101718950	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv981839	chr7:101632578-101663728	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv966867	chr7:101645987-101658423	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs202147	C7orf59	cis	parietal	SCAN
rs202147	ATXN7L1	cis	cerebellum	SCAN
rs202147	PVRIG	cis	cerebellum	SCAN
rs202147	LMTK2	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101578200-101671200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:101627000-101671200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:101628000-101651600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr7:101629000-101651600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:101630000-101668000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr7:101630800-101652400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:101633400-101651400	Weak transcription	Gastric	stomach
8	chr7:101634400-101651600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr7:101634600-101652000	Weak transcription	Primary T cells from cord blood	blood
10	chr7:101635000-101652000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr7:101635800-101651400	Weak transcription	HepG2	liver
12	chr7:101639800-101655800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:101640200-101651600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr7:101640200-101652000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:101641600-101672000	Weak transcription	K562	blood
16	chr7:101641800-101651800	Weak transcription	Fetal Intestine Large	intestine
17	chr7:101642000-101661600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr7:101642200-101666600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr7:101642200-101671400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr7:101642200-101671600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr7:101642200-101674600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr7:101642400-101652200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr7:101642400-101661800	Weak transcription	Spleen	Spleen
24	chr7:101642400-101668000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr7:101642400-101671200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr7:101642400-101671400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr7:101642400-101675400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr7:101642800-101651600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr7:101642800-101668000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr7:101642800-101697600	Weak transcription	Primary B cells from cord blood	blood
31	chr7:101643000-101655600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr7:101643000-101657400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr7:101643000-101665200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr7:101643000-101672800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr7:101643000-101675600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr7:101643200-101651400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr7:101643200-101652400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr7:101643200-101666400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr7:101644000-101651400	Weak transcription	Placenta	Placenta
40	chr7:101644000-101651800	Weak transcription	Thymus	Thymus
41	chr7:101644000-101652800	Weak transcription	HSMMtube	muscle
42	chr7:101644200-101651400	Weak transcription	Esophagus	oesophagus
43	chr7:101644200-101651800	Weak transcription	Right Ventricle	heart
44	chr7:101644200-101661800	Weak transcription	Right Atrium	heart
45	chr7:101644400-101652200	Weak transcription	Dnd41	blood
46	chr7:101644400-101657400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr7:101644600-101651600	Weak transcription	Fetal Heart	heart
48	chr7:101645800-101653600	Strong transcription	Fetal Intestine Small	intestine
49	chr7:101646800-101651600	Weak transcription	Pancreas	Pancrea
50	chr7:101646800-101671600	Weak transcription	GM12878-XiMat	blood

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