Variant report

Variant	rs7194091
Chromosome Location	chr16:70786780-70786781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr16:70786137-70787250	PBDE	blood:	n/a	chr16:70786490-70786507 chr16:70786499-70786508

No.	Distal block	Cell Line	Cell type
1	chr16:70780242..70783791-chr16:70785979..70788934,3	K562	blood:
2	chr16:70781579..70783780-chr16:70785789..70787753,2	K562	blood:
3	chr16:70718829..70721529-chr16:70784921..70786790,2	MCF-7	breast:
4	chr16:70690639..70692190-chr16:70786277..70788238,2	MCF-7	breast:
5	chr16:70785497..70787699-chr16:70811654..70814215,2	MCF-7	breast:
6	chr16:70747966..70750643-chr16:70785979..70788271,2	MCF-7	breast:

Variant related genes	Relation type
VAC14-AS1	TF binding region
ENSG00000132613	Chromatin interaction
ENSG00000260156	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1009285	0.87[ASN][1000 genomes]
rs11866379	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12920588	0.82[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs12924064	0.82[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs12926985	0.81[ASN][1000 genomes]
rs12934723	0.81[ASN][1000 genomes]
rs12935645	0.81[ASN][1000 genomes]
rs1551528	0.92[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1551529	0.92[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs16970484	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16970513	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17248914	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290614	1.00[CEU][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs28676580	0.91[ASN][1000 genomes]
rs2902830	1.00[CEU][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs34268521	0.83[ASN][1000 genomes]
rs35665975	0.87[ASN][1000 genomes]
rs3743988	0.93[CEU][hapmap]
rs3760118	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3855651	0.91[ASN][1000 genomes]
rs4985364	0.93[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap];0.91[ASN][1000 genomes]
rs4985423	0.93[CEU][hapmap];0.83[TSI][hapmap]
rs4985425	0.91[ASN][1000 genomes]
rs52826576	0.87[ASN][1000 genomes]
rs6499335	1.00[CEU][hapmap];0.80[MEX][hapmap]
rs6499336	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs7185921	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7188712	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7196225	1.00[ASN][1000 genomes]
rs7202363	0.86[CHD][hapmap];0.88[JPT][hapmap]
rs7203578	0.93[CEU][hapmap];0.83[TSI][hapmap]
rs74024449	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8044133	0.81[ASN][1000 genomes]
rs8052615	0.81[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap]
rs8060947	0.93[CEU][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap]
rs9931380	0.81[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.84[MEX][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	nsv517391	chr16:70666410-70840490	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv457517	chr16:70666722-70840490	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv572945	chr16:70666722-70840490	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv906879	chr16:70677785-70790831	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv906880	chr16:70677785-70796515	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers 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 miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv906889	chr16:70724001-70790831	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv906890	chr16:70740707-70790831	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1061191	chr16:70754975-71201367	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
9	nsv1059478	chr16:70773597-71237055	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7194091	TPPP3	cis	parietal	SCAN
rs7194091	ELMO3	cis	cerebellum	SCAN
rs7194091	VAC14	cis	lymphoblastoid	seeQTL
rs7194091	CENPT	cis	parietal	SCAN
rs7194091	VAC14	cis	Lymphoblastoid	GTEx
rs7194091	VAC14	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70772600-70813400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr16:70773000-70805600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr16:70773000-70815800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr16:70773400-70816200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr16:70777800-70788400	Enhancers	Psoas Muscle	Psoas
6	chr16:70778400-70788200	Enhancers	Liver	Liver
7	chr16:70778800-70787000	Enhancers	Fetal Thymus	thymus
8	chr16:70778800-70788000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr16:70779000-70788600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr16:70779200-70787400	Enhancers	Lung	lung
11	chr16:70779400-70786800	Enhancers	Colonic Mucosa	Colon
12	chr16:70779400-70786800	Enhancers	Gastric	stomach
13	chr16:70779400-70787000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr16:70779400-70787600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr16:70779400-70787800	Enhancers	Esophagus	oesophagus
16	chr16:70779400-70791600	Weak transcription	Dnd41	blood
17	chr16:70779600-70787800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr16:70779600-70788200	Enhancers	Adipose Nuclei	Adipose
19	chr16:70779800-70787200	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr16:70779800-70788000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr16:70780000-70789800	Genic enhancers	Fetal Stomach	stomach
22	chr16:70781200-70791600	Weak transcription	Aorta	Aorta
23	chr16:70781200-70794200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr16:70781200-70798600	Weak transcription	Hela-S3	cervix
25	chr16:70781200-70826800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr16:70781400-70788000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr16:70781600-70789000	Enhancers	Brain Cingulate Gyrus	brain
28	chr16:70781800-70815000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr16:70782000-70791400	Weak transcription	GM12878-XiMat	blood
30	chr16:70782200-70788400	Enhancers	Stomach Mucosa	stomach
31	chr16:70782600-70786800	Enhancers	Fetal Kidney	kidney
32	chr16:70782600-70787400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr16:70782600-70792800	Weak transcription	K562	blood
34	chr16:70782800-70787400	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr16:70782800-70790000	Weak transcription	HMEC	breast
36	chr16:70783400-70787000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr16:70783400-70787400	Enhancers	Ovary	ovary
38	chr16:70783400-70788200	Genic enhancers	Fetal Muscle Leg	muscle
39	chr16:70783400-70788600	Genic enhancers	Spleen	Spleen
40	chr16:70783400-70794400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr16:70783600-70787400	Enhancers	Primary hematopoietic stem cells	blood
42	chr16:70783600-70789200	Weak transcription	NHEK	skin
43	chr16:70783800-70788200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr16:70783800-70788200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr16:70783800-70797000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr16:70784000-70787400	Enhancers	Placenta	Placenta
47	chr16:70784200-70786800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr16:70784200-70787000	Enhancers	Right Ventricle	heart
49	chr16:70784200-70790600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr16:70784200-70794200	Weak transcription	Small Intestine	intestine

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