Variant report

Variant	rs16970484
Chromosome Location	chr16:70785969-70785970
allele	C/G
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	MYC	chr16:70784803-70786100	NB4	blood:	n/a	chr16:70785543-70785552

No.	Distal block	Cell Line	Cell type
1	chr16:70773737..70776366-chr16:70784353..70786152,2	K562	blood:
2	chr16:70781579..70783780-chr16:70785789..70787753,2	K562	blood:
3	chr16:70718829..70721529-chr16:70784921..70786790,2	MCF-7	breast:
4	chr16:70687934..70690062-chr16:70784015..70786102,2	K562	blood:
5	chr16:70785497..70787699-chr16:70811654..70814215,2	MCF-7	breast:

Variant related genes	Relation type
VAC14-AS1	TF binding region
ENSG00000157368	Chromatin interaction
ENSG00000132613	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1009285	0.85[ASN][1000 genomes]
rs11864614	0.89[JPT][hapmap]
rs11866379	1.00[JPT][hapmap]
rs12920588	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12924064	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12928270	0.82[ASN][1000 genomes]
rs12929374	0.80[ASN][1000 genomes]
rs1551528	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1551529	0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16970513	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17248914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290614	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs28676580	0.93[ASN][1000 genomes]
rs2902830	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34268521	0.81[ASN][1000 genomes]
rs35665975	0.85[ASN][1000 genomes]
rs3743988	0.93[CEU][hapmap]
rs3760118	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3855651	0.89[ASN][1000 genomes]
rs4985364	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4985423	0.93[CEU][hapmap]
rs4985425	0.93[ASN][1000 genomes]
rs52826576	0.85[ASN][1000 genomes]
rs6499335	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6499336	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs713511	0.82[ASN][1000 genomes]
rs71401831	0.81[ASN][1000 genomes]
rs7185921	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7188712	0.92[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7194091	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]
rs7196225	0.98[ASN][1000 genomes]
rs7202363	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7203578	0.93[CEU][hapmap]
rs74024449	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052615	0.81[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs8060947	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9931380	0.81[CEU][hapmap];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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16970484	VAC14	cis	Lymphoblastoid	GTEx

Chromatin state (count:123 , 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	chr16:70779000-70786200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr16:70779000-70786400	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr16:70779000-70786400	Enhancers	NHDF-Ad	bronchial
12	chr16:70779000-70788600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr16:70779200-70787400	Enhancers	Lung	lung
14	chr16:70779400-70786200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr16:70779400-70786800	Enhancers	Colonic Mucosa	Colon
16	chr16:70779400-70786800	Enhancers	Gastric	stomach
17	chr16:70779400-70787000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr16:70779400-70787600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr16:70779400-70787800	Enhancers	Esophagus	oesophagus
20	chr16:70779400-70791600	Weak transcription	Dnd41	blood
21	chr16:70779600-70786200	Genic enhancers	Fetal Intestine Small	intestine
22	chr16:70779600-70786600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr16:70779600-70787800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr16:70779600-70788200	Enhancers	Adipose Nuclei	Adipose
25	chr16:70779800-70786400	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr16:70779800-70787200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr16:70779800-70788000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr16:70780000-70786600	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr16:70780000-70789800	Genic enhancers	Fetal Stomach	stomach
30	chr16:70781200-70791600	Weak transcription	Aorta	Aorta
31	chr16:70781200-70794200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr16:70781200-70798600	Weak transcription	Hela-S3	cervix
33	chr16:70781200-70826800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr16:70781400-70788000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr16:70781600-70789000	Enhancers	Brain Cingulate Gyrus	brain
36	chr16:70781800-70786600	Enhancers	Fetal Muscle Trunk	muscle
37	chr16:70781800-70815000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr16:70782000-70791400	Weak transcription	GM12878-XiMat	blood
39	chr16:70782200-70788400	Enhancers	Stomach Mucosa	stomach
40	chr16:70782600-70786800	Enhancers	Fetal Kidney	kidney
41	chr16:70782600-70787400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr16:70782600-70792800	Weak transcription	K562	blood
43	chr16:70782800-70787400	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr16:70782800-70790000	Weak transcription	HMEC	breast
45	chr16:70783200-70786000	Enhancers	Brain Substantia Nigra	brain
46	chr16:70783200-70786400	Enhancers	Fetal Lung	lung
47	chr16:70783400-70786000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr16:70783400-70786000	Enhancers	Colon Smooth Muscle	Colon
49	chr16:70783400-70786600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr16:70783400-70787000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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