Variant report

Variant	rs716886
Chromosome Location	chr15:83715853-83715854
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:83714861..83717346-chr15:83721715..83724046,2	K562	blood:
2	chr15:83715559..83717432-chr15:83875352..83877584,2	MCF-7	breast:
3	chr15:83710008..83713519-chr15:83714688..83717588,4	K562	blood:
4	chr15:83715424..83718064-chr15:83719632..83721624,3	K562	blood:
5	chr15:83714280..83716430-chr15:83733917..83736956,4	MCF-7	breast:
6	chr15:83712066..83714365-chr15:83715736..83718264,3	MCF-7	breast:
7	chr15:83715424..83717754-chr15:83719632..83721290,2	K562	blood:
8	chr15:83677538..83680423-chr15:83715365..83717116,2	K562	blood:
9	chr15:83709446..83712145-chr15:83714233..83716291,3	MCF-7	breast:
10	chr15:83711130..83713697-chr15:83715382..83717588,2	K562	blood:
11	chr15:83678274..83681051-chr15:83713533..83717872,4	MCF-7	breast:
12	chr15:83714522..83717399-chr15:83720662..83723251,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259308	Chromatin interaction
ENSG00000166503	Chromatin interaction
ENSG00000064726	Chromatin interaction
ENSG00000169609	Chromatin interaction
ENSG00000263643	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1010820	0.85[GIH][hapmap]
rs11857990	1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs11858468	0.85[GIH][hapmap]
rs12440265	0.84[GIH][hapmap]
rs12441585	0.85[TSI][hapmap]
rs17158080	0.82[TSI][hapmap]
rs17295457	1.00[CHD][hapmap]
rs17361375	0.85[GIH][hapmap]
rs28429062	1.00[CHD][hapmap]
rs28662361	1.00[CHD][hapmap]
rs28711332	1.00[CHD][hapmap]
rs6603042	0.86[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes]
rs6603047	0.81[TSI][hapmap]
rs7170046	1.00[CHD][hapmap]
rs7177462	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180407	0.82[TSI][hapmap]
rs8027193	0.82[TSI][hapmap]
rs8031723	0.85[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs716886	TM6SF1	cis	cerebellum	SCAN
rs716886	BTBD1	cis	parietal	SCAN
rs716886	C15orf40	cis	parietal	SCAN
rs716886	WHAMM	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83681600-83732000	Weak transcription	Stomach Mucosa	stomach
2	chr15:83683000-83723000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:83683400-83726600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:83697800-83721000	Strong transcription	Fetal Intestine Large	intestine
5	chr15:83699000-83716800	Weak transcription	Aorta	Aorta
6	chr15:83699000-83725800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:83700400-83734400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:83701600-83732800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:83705000-83720800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:83705000-83725800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:83705000-83731000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr15:83705200-83720000	Strong transcription	Dnd41	blood
13	chr15:83705600-83721400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:83706000-83725400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:83706600-83718000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr15:83706800-83726600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr15:83707000-83725400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr15:83707400-83718400	Strong transcription	Fetal Muscle Leg	muscle
19	chr15:83707400-83725400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:83707800-83719200	Strong transcription	GM12878-XiMat	blood
21	chr15:83708000-83718000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:83708000-83718200	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr15:83708000-83722000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:83708000-83725400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr15:83708600-83719800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr15:83708600-83726000	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr15:83708800-83726400	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr15:83708800-83726600	Weak transcription	Pancreas	Pancrea
29	chr15:83709000-83726600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:83709000-83726600	Weak transcription	Fetal Brain Male	brain
31	chr15:83709200-83716200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr15:83709200-83724400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr15:83709200-83727000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:83709600-83730800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr15:83710400-83716200	Weak transcription	Psoas Muscle	Psoas
36	chr15:83710400-83722800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:83710600-83716200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr15:83710600-83716200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr15:83710600-83716200	Weak transcription	Fetal Heart	heart
40	chr15:83710600-83716600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr15:83710600-83716800	Weak transcription	Fetal Kidney	kidney
42	chr15:83710600-83717200	Weak transcription	Ovary	ovary
43	chr15:83710600-83717800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:83710600-83722000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:83710600-83723800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr15:83710600-83723800	Weak transcription	Brain Angular Gyrus	brain
47	chr15:83710600-83730200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:83710600-83730200	Weak transcription	Esophagus	oesophagus
49	chr15:83710800-83716400	Weak transcription	Spleen	Spleen
50	chr15:83710800-83716800	Weak transcription	Fetal Lung	lung

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