Variant report

Variant	rs4948367
Chromosome Location	chr10:61573386-61573387
allele	A/C
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	chr10:61573293-61573765	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
CCDC6	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10509114	1.00[CHD][hapmap]
rs10994001	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10994058	0.89[CHD][hapmap]
rs1127327	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12250019	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12250305	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12256258	0.88[EUR][1000 genomes]
rs12569631	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12571632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12573055	0.82[CHB][hapmap]
rs12573796	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17199652	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17199988	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17201105	0.86[CHB][hapmap]
rs17202345	1.00[CHD][hapmap]
rs17789329	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17790289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17790901	0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[TSI][hapmap]
rs17791132	0.86[CHB][hapmap]
rs17791436	0.86[CHB][hapmap]
rs17791484	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs2175913	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271561	0.86[CHB][hapmap]
rs2271564	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2393567	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4597020	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4948238	0.85[JPT][hapmap]
rs4948368	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs56232063	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56247613	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72815892	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72815897	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72817909	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72817910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72817915	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73269619	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv975776	chr10:61569234-61574091	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4948367	SLC16A9	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:61537600-61582800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:61549600-61579600	Strong transcription	Primary B cells from cord blood	blood
3	chr10:61556000-61583800	Strong transcription	Primary B cells from peripheral blood	blood
4	chr10:61556200-61573800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr10:61556200-61573800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr10:61556200-61574800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr10:61556200-61574800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr10:61556800-61574600	Strong transcription	Primary T cells from cord blood	blood
9	chr10:61557400-61573400	Strong transcription	Adipose Nuclei	Adipose
10	chr10:61557400-61574600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr10:61561000-61574000	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr10:61561000-61574600	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr10:61561200-61574000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr10:61561200-61574600	Strong transcription	HepG2	liver
15	chr10:61561600-61573600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr10:61562000-61573400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr10:61562200-61574600	Strong transcription	Fetal Thymus	thymus
18	chr10:61562600-61573400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr10:61562800-61574200	Strong transcription	Placenta	Placenta
20	chr10:61562800-61574400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr10:61563600-61577600	Weak transcription	Right Atrium	heart
22	chr10:61564200-61576800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr10:61565000-61573600	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr10:61565400-61586600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr10:61567000-61593600	Weak transcription	Small Intestine	intestine
26	chr10:61567600-61579200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr10:61568200-61582400	Weak transcription	Psoas Muscle	Psoas
28	chr10:61569000-61574600	Strong transcription	Primary hematopoietic stem cells	blood
29	chr10:61569200-61574600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr10:61569400-61574000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr10:61569400-61574400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr10:61569400-61575000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr10:61569600-61573600	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr10:61569600-61574200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr10:61569600-61574400	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr10:61569600-61574600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr10:61569800-61573600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr10:61569800-61574800	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr10:61570000-61574400	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr10:61570000-61575000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr10:61570200-61574800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr10:61571000-61576800	Weak transcription	Fetal Intestine Small	intestine
43	chr10:61571000-61591200	Weak transcription	NHEK	skin
44	chr10:61571200-61577600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr10:61571400-61579000	Weak transcription	Brain Germinal Matrix	brain
46	chr10:61571400-61628000	Weak transcription	Spleen	Spleen
47	chr10:61571600-61574000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr10:61571600-61574200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr10:61571600-61574200	Weak transcription	Stomach Mucosa	stomach
50	chr10:61571600-61574400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links