Variant report

Variant	rs3813908
Chromosome Location	chr16:70712549-70712550
allele	G/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	POLR2A	chr16:70709478-70713336	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:70711953-70712986	HepG2	liver:	n/a	n/a
3	POLR2A	chr16:70707751-70721480	HepG2	liver:	n/a	n/a
4	POLR2A	chr16:70712210-70713293	HepG2	liver:	n/a	n/a
5	POLR2A	chr16:70712475-70712695	K562	blood:	n/a	n/a
6	POLR2A	chr16:70709715-70712897	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:70710502..70716221-chr16:70726302..70731102,7	K562	blood:
2	chr16:70709373..70712593-chr16:70717107..70721470,4	MCF-7	breast:
3	chr16:70710951..70713595-chr16:70779027..70782774,3	MCF-7	breast:

Variant related genes	Relation type
MTSS1L	TF binding region
ENSG00000132613	Chromatin interaction
ENSG00000260156	Chromatin interaction
ENSG00000103043	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12599280	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2054183	0.89[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap]
rs2242126	0.87[MEX][hapmap]
rs35566469	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985563	0.87[MEX][hapmap]
rs7194558	0.83[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7195695	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8048078	0.83[MEX][hapmap]
rs8059238	0.84[GIH][hapmap]
rs936301	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv906874	chr16:70677785-70740707	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv906875	chr16:70677785-70742536	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv906876	chr16:70677785-70757555	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv906877	chr16:70677785-70766378	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv906878	chr16:70677785-70782922	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	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
10	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
11	nsv906882	chr16:70690989-70725815	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
12	nsv572946	chr16:70694000-70740707	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
13	nsv471094	chr16:70694000-70749970	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
14	nsv906884	chr16:70696009-70725815	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
15	nsv906885	chr16:70696367-70742536	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
16	nsv1059226	chr16:70708698-70779144	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
17	nsv906886	chr16:70712549-70727324	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3813908	TMED6	cis	cerebellum	SCAN
rs3813908	RLTPR	cis	cerebellum	SCAN
rs3813908	EXOC3L	cis	cerebellum	SCAN
rs3813908	PSKH1	cis	cerebellum	SCAN
rs3813908	IL34	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70688400-70715000	Weak transcription	Stomach Mucosa	stomach
2	chr16:70694600-70720200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:70695600-70712600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr16:70695600-70714200	Strong transcription	Placenta	Placenta
5	chr16:70695600-70714400	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr16:70695600-70714400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr16:70695600-70714400	Strong transcription	Lung	lung
8	chr16:70695600-70714600	Strong transcription	Liver	Liver
9	chr16:70695800-70713800	Strong transcription	Fetal Intestine Large	intestine
10	chr16:70695800-70714200	Strong transcription	NHDF-Ad	bronchial
11	chr16:70696000-70714200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr16:70696000-70714200	Strong transcription	Fetal Thymus	thymus
13	chr16:70696400-70713400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr16:70696400-70714200	Strong transcription	Fetal Intestine Small	intestine
15	chr16:70696600-70713400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr16:70696600-70714200	Strong transcription	Fetal Lung	lung
17	chr16:70696800-70713600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr16:70696800-70714200	Strong transcription	Osteobl	bone
19	chr16:70697200-70713400	Strong transcription	Adipose Nuclei	Adipose
20	chr16:70697400-70713400	Strong transcription	A549	lung
21	chr16:70697600-70713000	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr16:70697600-70713600	Strong transcription	Fetal Stomach	stomach
23	chr16:70697600-70713600	Strong transcription	Ovary	ovary
24	chr16:70697600-70713800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr16:70697600-70714200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr16:70698000-70713200	Strong transcription	HSMMtube	muscle
27	chr16:70698000-70714400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr16:70698800-70713400	Strong transcription	NHLF	lung
29	chr16:70699600-70713400	Strong transcription	HSMM	muscle
30	chr16:70700400-70718800	Weak transcription	Small Intestine	intestine
31	chr16:70701000-70714200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr16:70702200-70712800	Strong transcription	Pancreatic Islets	Pancreatic Islet
33	chr16:70703000-70712800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr16:70703000-70713200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr16:70703000-70713600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr16:70703000-70715200	Strong transcription	Thymus	Thymus
37	chr16:70703000-70717800	Weak transcription	Hela-S3	cervix
38	chr16:70703200-70714400	Strong transcription	Brain Germinal Matrix	brain
39	chr16:70703200-70714400	Strong transcription	Fetal Brain Female	brain
40	chr16:70703400-70713800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr16:70703400-70714400	Strong transcription	HepG2	liver
42	chr16:70703800-70714600	Strong transcription	Dnd41	blood
43	chr16:70704600-70712600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr16:70704600-70714200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr16:70704600-70715400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr16:70704800-70714200	Weak transcription	Fetal Brain Male	brain
47	chr16:70705200-70715200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr16:70705600-70713400	Strong transcription	Brain Hippocampus Middle	brain
49	chr16:70705800-70715400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr16:70706600-70712600	Strong transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links