Variant report

Variant	rs10946770
Chromosome Location	chr6:25403432-25403433
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	MAFK	chr6:25403375-25403584	HepG2	liver:	n/a	chr6:25403530-25403545 chr6:25403478-25403493
2	SPI1	chr6:25403359-25403649	GM12878	blood:	n/a	n/a
3	MAFK	chr6:25403365-25403585	HepG2	liver:	n/a	chr6:25403530-25403545 chr6:25403478-25403493

Variant related genes	Relation type
ENSG00000253017	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12201737	0.94[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716796	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs716798	0.81[EUR][1000 genomes]
rs880225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461152	0.81[EUR][1000 genomes]
rs9461153	0.82[EUR][1000 genomes]
rs9467501	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10946770	LRRC16	cis	multi-tissue	Pritchard
rs10946770	LRRC16	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25377400-25410600	Weak transcription	Gastric	stomach
2	chr6:25383000-25403600	Weak transcription	Right Atrium	heart
3	chr6:25383600-25405000	Weak transcription	Fetal Intestine Small	intestine
4	chr6:25389400-25403600	Weak transcription	Thymus	Thymus
5	chr6:25390200-25405000	Weak transcription	Adipose Nuclei	Adipose
6	chr6:25391400-25403800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr6:25394400-25403600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr6:25396000-25403600	Weak transcription	Primary T cells from cord blood	blood
9	chr6:25397600-25405600	Weak transcription	Stomach Mucosa	stomach
10	chr6:25397800-25403600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:25397800-25403800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:25397800-25403800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:25397800-25404200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:25397800-25404400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:25397800-25404400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:25398000-25403600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:25398000-25404200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:25399000-25403600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:25399000-25404200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:25399000-25405200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:25399200-25404400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:25399400-25403600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:25399600-25403600	Weak transcription	Small Intestine	intestine
24	chr6:25402000-25404400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:25402200-25403600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:25402200-25403600	Weak transcription	Spleen	Spleen
27	chr6:25402200-25404600	Weak transcription	Aorta	Aorta
28	chr6:25402200-25405000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:25402200-25405000	Weak transcription	NHEK	skin
30	chr6:25402200-25405200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:25402200-25405200	Weak transcription	HMEC	breast
32	chr6:25402200-25406200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:25402200-25409600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:25402400-25403600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr6:25402400-25405000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:25402600-25404200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr6:25403200-25403600	Weak transcription	Pancreas	Pancrea
38	chr6:25403200-25404400	Enhancers	GM12878-XiMat	blood
39	chr6:25403200-25404600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:25403200-25404800	Enhancers	Primary B cells from peripheral blood	blood
41	chr6:25403400-25403800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr6:25403400-25404400	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr6:25403400-25404400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:25403400-25404800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:25403400-25404800	Enhancers	Fetal Thymus	thymus
46	chr6:25403400-25405000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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