Variant report

Variant	rs12705070
Chromosome Location	chr7:99656927-99656928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99655903..99659149-chr7:99676260..99680266,4	K562	blood:
2	chr7:99648921..99651370-chr7:99655512..99657168,2	K562	blood:
3	chr7:99655564..99657168-chr7:99714504..99716698,2	MCF-7	breast:
4	chr7:99656182..99658433-chr7:99660144..99662417,2	K562	blood:
5	chr7:99656025..99659338-chr7:99698402..99700947,3	K562	blood:
6	chr7:99650255..99652403-chr7:99656167..99658758,2	K562	blood:
7	chr7:99656375..99658370-chr7:99722695..99724630,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221838	Chromatin interaction
ENSG00000106290	Chromatin interaction
ENSG00000166508	Chromatin interaction
ENSG00000166526	Chromatin interaction
ENSG00000214309	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1015538	0.80[ASN][1000 genomes]
rs10228764	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10267212	0.82[CEU][hapmap];0.82[GIH][hapmap]
rs10281368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1060544	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1076237	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs11764584	0.85[YRI][hapmap]
rs11771139	0.83[CHB][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap]
rs11771331	0.90[MEX][hapmap];0.93[YRI][hapmap]
rs12705071	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs13223792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13232115	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1534310	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1880949	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs1963304	0.80[ASN][1000 genomes]
rs2070215	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2293479	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs34031156	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35146811	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs3823646	0.85[YRI][hapmap]
rs4134903	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4424195	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4729566	0.90[MEX][hapmap];0.93[YRI][hapmap];0.80[ASN][1000 genomes]
rs4729567	0.86[YRI][hapmap]
rs4729576	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59261051	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6465760	0.82[CEU][hapmap];0.82[GIH][hapmap]
rs6465761	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6465762	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6950205	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6953441	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6974305	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7788746	0.90[MEX][hapmap];0.93[YRI][hapmap];0.80[ASN][1000 genomes]
rs7807641	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12705070	GATS	cis	cerebellum	SCAN
rs12705070	TAF6	cis	Thyroid	GTEx
rs12705070	GAL3ST4	cis	cerebellum	SCAN
rs12705070	ZSCAN21	cis	parietal	SCAN
rs12705070	BUD31	cis	parietal	SCAN
rs12705070	SERPINE1	cis	cerebellum	SCAN
rs12705070	GATS	cis	parietal	SCAN
rs12705070	ZKSCAN1	cis	cerebellum	SCAN
rs12705070	LRRC17	cis	parietal	SCAN
rs12705070	ZNF498	cis	cerebellum	SCAN
rs12705070	PILRB	cis	parietal	SCAN
rs12705070	GATS	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99648400-99661400	Weak transcription	Small Intestine	intestine
2	chr7:99648400-99667600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:99648400-99667600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:99648400-99667600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr7:99648400-99667800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr7:99648400-99668000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr7:99648600-99660600	Weak transcription	HSMM	muscle
8	chr7:99648600-99663400	Weak transcription	Stomach Mucosa	stomach
9	chr7:99652600-99659000	Strong transcription	Fetal Muscle Leg	muscle
10	chr7:99653400-99666400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:99653800-99658800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr7:99653800-99660200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:99653800-99663000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:99653800-99663200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:99653800-99664200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr7:99653800-99667600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:99654000-99657200	Strong transcription	Brain Substantia Nigra	brain
18	chr7:99654000-99658000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr7:99654000-99658000	Strong transcription	Fetal Intestine Large	intestine
20	chr7:99654000-99662200	Strong transcription	Fetal Stomach	stomach
21	chr7:99654000-99663600	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr7:99654000-99663800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:99654000-99664000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr7:99654000-99668000	Strong transcription	Fetal Brain Female	brain
25	chr7:99654200-99663000	Strong transcription	Stomach Smooth Muscle	stomach
26	chr7:99654200-99663600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr7:99654200-99666400	Strong transcription	Fetal Intestine Small	intestine
28	chr7:99654200-99667400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr7:99654400-99657000	Strong transcription	Primary T cells from cord blood	blood
30	chr7:99654400-99657400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr7:99654400-99657600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:99654400-99657600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr7:99654400-99658000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr7:99654400-99658000	Strong transcription	HSMMtube	muscle
35	chr7:99654400-99659000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr7:99654400-99661600	Strong transcription	A549	lung
37	chr7:99654400-99662200	Strong transcription	Fetal Lung	lung
38	chr7:99654400-99662400	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr7:99654400-99663000	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr7:99654400-99664000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr7:99654400-99667600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr7:99654400-99667600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr7:99654400-99667600	Strong transcription	Brain Germinal Matrix	brain
44	chr7:99654400-99668400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr7:99654600-99657000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr7:99654600-99657000	Strong transcription	Gastric	stomach
47	chr7:99654600-99657200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr7:99654600-99657200	Strong transcription	Aorta	Aorta
49	chr7:99654600-99657200	Strong transcription	Brain Cingulate Gyrus	brain
50	chr7:99654600-99657200	Strong transcription	NHEK	skin

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