Variant report

Variant	rs12705073
Chromosome Location	chr7:99774122-99774123
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr7:99773789-99775353	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr7:99773711-99774318	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr7:99773762-99774206	SK-N-MC	brain:	n/a	n/a
4	MXI1	chr7:99773856-99776076	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr7:99773822-99774548	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr7:99774078-99775211	H1-neurons	neurons:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99723966..99726705-chr7:99773626..99776513,3	K562	blood:
2	chr7:99754180..99757947-chr7:99773944..99778293,5	K562	blood:
3	chr7:99767272..99770756-chr7:99771153..99775151,5	MCF-7	breast:
4	chr7:99687387..99689514-chr7:99773501..99775690,2	MCF-7	breast:
5	chr7:99763454..99766181-chr7:99772749..99774869,2	K562	blood:
6	chr7:99767104..99770027-chr7:99772999..99775636,2	MCF-7	breast:
7	chr7:99753430..99757124-chr7:99772344..99777147,8	MCF-7	breast:
8	chr7:99771880..99773648-chr7:99773808..99775358,2	MCF-7	breast:
9	chr7:99755258..99758996-chr7:99773394..99775783,3	MCF-7	breast:
10	chr7:99751463..99761050-chr7:99772463..99778676,10	K562	blood:
11	chr16:88796831..88799355-chr7:99773694..99775214,2	K562	blood:
12	chr7:99717080..99719832-chr7:99772182..99775023,2	MCF-7	breast:

No data

Variant related genes	Relation type
GPC2	TF binding region
STAG3	TF binding region
ENSG00000224888	Chromatin interaction
ENSG00000166997	Chromatin interaction
ENSG00000266154	Chromatin interaction
ENSG00000106290	Chromatin interaction
ENSG00000214309	Chromatin interaction
ENSG00000242798	Chromatin interaction
ENSG00000213420	Chromatin interaction
ENSG00000146826	Chromatin interaction
ENSG00000197093	Chromatin interaction
ENSG00000168090	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10231604	0.85[LWK][hapmap]
rs1043915	0.86[CHB][hapmap]
rs1061230	0.86[CHB][hapmap]
rs10953295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1138417	0.86[CHB][hapmap]
rs11764176	0.86[CHB][hapmap];0.80[YRI][hapmap]
rs12666425	0.86[CHB][hapmap]
rs1623264	0.86[CHB][hapmap]
rs1624099	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1636975	0.86[CHB][hapmap]
rs1637001	0.86[CHB][hapmap]
rs1727128	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1727129	0.96[CEU][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1727133	0.86[CHB][hapmap]
rs1727134	0.86[CHB][hapmap]
rs1727138	0.86[CHB][hapmap]
rs1727140	0.86[CHB][hapmap]
rs1727143	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1727145	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1859787	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1918353	0.85[JPT][hapmap];0.88[LWK][hapmap]
rs2246713	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2272337	0.90[LWK][hapmap]
rs2405442	0.82[CHB][hapmap]
rs2528900	0.86[CHB][hapmap]
rs2906646	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2950518	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2950520	0.86[CHB][hapmap]
rs3735241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3735242	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3736590	0.88[LWK][hapmap]
rs3779045	0.86[CHB][hapmap]
rs3800951	0.80[LWK][hapmap]
rs4299940	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4729580	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66809776	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6948729	0.86[CHB][hapmap]
rs705867	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7794170	0.86[CHB][hapmap]
rs7799441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7811662	0.86[CHB][hapmap]
rs858502	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs858506	0.86[CHB][hapmap]
rs858510	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs858513	0.86[CHB][hapmap]
rs866500	0.86[CHB][hapmap]
rs941287	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases
3	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
4	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
5	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
6	nsv427794	chr7:99750981-99960900	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv428180	chr7:99750981-99960900	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Genic enhancers 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	51 gene(s)	inside rSNPs	diseases
8	nsv5867	chr7:99766774-99799755	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12705073	C17orf59	trans	cerebellum	SCAN
rs12705073	AP4M1	cis	cerebellum	SCAN
rs12705073	AP4M1	cis	Thyroid	GTEx
rs12705073	AZGP1	cis	parietal	SCAN
rs12705073	MBLAC1	cis	cerebellum	SCAN
rs12705073	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs12705073	PILRB	cis	cerebellum	SCAN
rs12705073	PVRIG	cis	lymphoblastoid	seeQTL
rs12705073	AP4M1	cis	lymphoblastoid	seeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99766800-99774200	Weak transcription	Fetal Lung	lung
2	chr7:99769600-99774200	Weak transcription	HMEC	breast
3	chr7:99769600-99774600	Weak transcription	Ovary	ovary
4	chr7:99769600-99774600	Weak transcription	Right Atrium	heart
5	chr7:99769800-99774200	Weak transcription	Primary B cells from cord blood	blood
6	chr7:99769800-99774200	Weak transcription	Brain Hippocampus Middle	brain
7	chr7:99769800-99774200	Weak transcription	NHDF-Ad	bronchial
8	chr7:99769800-99774600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:99770000-99774200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:99770000-99774200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr7:99770000-99774200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr7:99770000-99774200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr7:99770000-99774200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr7:99770000-99774200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr7:99770000-99774200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr7:99770000-99774200	Weak transcription	GM12878-XiMat	blood
17	chr7:99770000-99774400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr7:99770000-99774800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr7:99770000-99774800	Weak transcription	Spleen	Spleen
20	chr7:99773000-99774200	Weak transcription	Fetal Intestine Small	intestine
21	chr7:99773200-99774200	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr7:99773400-99774200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr7:99773400-99774600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr7:99773600-99774200	Enhancers	Thymus	Thymus
25	chr7:99773800-99774200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
26	chr7:99773800-99774200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:99773800-99774200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr7:99773800-99774200	Flanking Active TSS	Fetal Brain Female	brain
29	chr7:99773800-99774200	Enhancers	Fetal Muscle Leg	muscle
30	chr7:99773800-99774200	Enhancers	K562	blood
31	chr7:99773800-99774400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
32	chr7:99773800-99774400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:99773800-99774400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr7:99773800-99774400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr7:99773800-99774400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr7:99773800-99774400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr7:99773800-99774400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr7:99773800-99774400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr7:99773800-99774400	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr7:99773800-99774400	Enhancers	Primary hematopoietic stem cells	blood
41	chr7:99773800-99774400	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr7:99773800-99774400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:99773800-99774400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr7:99773800-99774400	Flanking Active TSS	Brain Germinal Matrix	brain
45	chr7:99773800-99774400	Flanking Active TSS	Fetal Brain Male	brain
46	chr7:99773800-99774600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr7:99773800-99774600	Enhancers	Primary T cells fromperipheralblood	blood
48	chr7:99773800-99774800	Flanking Active TSS	Fetal Thymus	thymus
49	chr7:99773800-99774800	Flanking Active TSS	Dnd41	blood
50	chr7:99773800-99775200	Active TSS	HUES48 Cell Line	embryonic stem cell

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