Variant report

Variant	rs10401713
Chromosome Location	chr19:19306147-19306148
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19305583..19307573-chr19:19309076..19310790,2	K562	blood:
2	chr19:19303809..19306527-chr19:19495529..19497596,2	K562	blood:
3	chr19:19304004..19306841-chr19:19429725..19433437,3	MCF-7	breast:
4	chr19:19294693..19300778-chr19:19301483..19306941,9	K562	blood:
5	chr19:19305757..19307573-chr19:19308012..19310576,2	K562	blood:

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction
ENSG00000129933	Chromatin interaction
ENSG00000254901	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000105705	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10403193	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10409380	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10409894	0.95[EUR][1000 genomes]
rs10412238	0.80[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10424365	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs1050483	0.90[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2283626	0.90[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28618105	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56007657	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7250569	0.84[GIH][hapmap];0.92[TSI][hapmap]
rs73537466	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv933613	chr19:19291456-19312244	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv961283	chr19:19293486-19312277	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv911304	chr19:19303802-19408164	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10401713	FAM129C	cis	parietal	SCAN
rs10401713	LRRC25	cis	parietal	SCAN
rs10401713	ZNF99	cis	parietal	SCAN
rs10401713	NCAN	cis	cerebellum	SCAN
rs10401713	FAM32A	cis	cerebellum	SCAN
rs10401713	OCEL1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19304200-19306200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr19:19304200-19306200	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr19:19304200-19306200	Enhancers	Fetal Brain Male	brain
4	chr19:19304200-19307000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:19304200-19307600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr19:19304200-19307800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:19304200-19307800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr19:19304200-19307800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:19304200-19307800	Weak transcription	Aorta	Aorta
10	chr19:19304200-19307800	Weak transcription	Fetal Brain Female	brain
11	chr19:19304200-19307800	Weak transcription	Ovary	ovary
12	chr19:19304200-19313400	Weak transcription	Fetal Kidney	kidney
13	chr19:19304200-19313400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr19:19304400-19306600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr19:19304400-19307600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:19304400-19307600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr19:19304400-19307800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:19304600-19306200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:19304600-19306400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr19:19304600-19307200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr19:19304600-19307200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr19:19304600-19307600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr19:19304600-19307800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr19:19304600-19312600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr19:19304800-19307200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:19304800-19307800	Weak transcription	Pancreas	Pancrea
27	chr19:19304800-19313000	Weak transcription	Stomach Mucosa	stomach
28	chr19:19304800-19313000	Weak transcription	HSMM	muscle
29	chr19:19304800-19313200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr19:19304800-19313600	Weak transcription	Small Intestine	intestine
31	chr19:19305000-19307000	Weak transcription	Fetal Intestine Large	intestine
32	chr19:19305000-19307200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:19305000-19307600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr19:19305000-19307600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr19:19305000-19307600	Weak transcription	Placenta	Placenta
36	chr19:19305000-19307600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr19:19305000-19307600	Weak transcription	A549	lung
38	chr19:19305000-19307600	Weak transcription	NHLF	lung
39	chr19:19305000-19307600	Weak transcription	Osteobl	bone
40	chr19:19305000-19307800	Weak transcription	Gastric	stomach
41	chr19:19305000-19307800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr19:19305000-19307800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr19:19305000-19310400	Weak transcription	HUVEC	blood vessel
44	chr19:19305000-19311000	Strong transcription	Fetal Thymus	thymus
45	chr19:19305000-19312400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr19:19305000-19312400	Weak transcription	HepG2	liver
47	chr19:19305000-19313400	Weak transcription	Fetal Heart	heart
48	chr19:19305200-19306200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr19:19305200-19306400	Enhancers	Adipose Nuclei	Adipose
50	chr19:19305200-19306800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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