Variant report

Variant	rs9917645
Chromosome Location	chr3:140683498-140683499
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:140678616-140684731	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:140680990..140685074-chr3:140687578..140691434,4	K562	blood:
2	chr3:140660122..140661654-chr3:140682941..140685773,2	K562	blood:
3	chr3:140672006..140672786-chr3:140682879..140683855,2	MCF-7	breast:
4	chr3:140659978..140662148-chr3:140682890..140685821,2	MCF-7	breast:
5	chr3:140680069..140681751-chr3:140681989..140683557,2	MCF-7	breast:
6	chr3:140682780..140684473-chr3:140693790..140695745,2	MCF-7	breast:
7	chr3:140659366..140662010-chr3:140681313..140684764,3	K562	blood:
8	chr3:140658799..140662032-chr3:140683166..140686698,4	MCF-7	breast:

No data

Variant related genes	Relation type
SLC25A36	TF binding region
ENSG00000114120	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1109284	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13099216	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13100471	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34267131	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34434275	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34605552	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34677627	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35633570	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6785188	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7616174	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7620524	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7628400	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7638025	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs878117	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][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	nsv591865	chr3:140396022-140728850	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1005522	chr3:140454632-140685915	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv536732	chr3:140454632-140685915	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv1793115	chr3:140663107-140693053	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140661800-140697200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:140662200-140696800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:140662400-140692200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:140662600-140696800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:140662800-140695800	Weak transcription	NHLF	lung
6	chr3:140663200-140692600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr3:140663200-140696000	Weak transcription	Fetal Stomach	stomach
8	chr3:140663400-140697400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:140663600-140692600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:140664200-140692400	Weak transcription	Fetal Brain Female	brain
11	chr3:140664200-140703800	Weak transcription	Aorta	Aorta
12	chr3:140665400-140698400	Weak transcription	Brain Germinal Matrix	brain
13	chr3:140665800-140697600	Weak transcription	Gastric	stomach
14	chr3:140670000-140692600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:140670000-140693800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:140670000-140697200	Weak transcription	Esophagus	oesophagus
17	chr3:140670600-140698200	Weak transcription	Spleen	Spleen
18	chr3:140670800-140696800	Weak transcription	Lung	lung
19	chr3:140671400-140694000	Weak transcription	Ovary	ovary
20	chr3:140672000-140694800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:140672200-140692000	Weak transcription	HUVEC	blood vessel
22	chr3:140672200-140699000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:140672600-140694200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:140672600-140695000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:140672800-140692800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:140672800-140698800	Weak transcription	Right Ventricle	heart
27	chr3:140672800-140700000	Weak transcription	Small Intestine	intestine
28	chr3:140673200-140694200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:140673400-140692800	Weak transcription	Brain Anterior Caudate	brain
30	chr3:140673400-140693400	Weak transcription	Fetal Intestine Small	intestine
31	chr3:140673400-140694000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:140673400-140698800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:140673400-140700200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:140673600-140683800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:140673600-140699000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr3:140673800-140694000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:140674400-140697200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:140674600-140687000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:140674800-140685000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:140674800-140692600	Weak transcription	Psoas Muscle	Psoas
41	chr3:140675000-140697600	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr3:140675200-140695200	Weak transcription	Fetal Brain Male	brain
43	chr3:140675200-140699000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:140675400-140684000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:140675400-140690600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:140675400-140690800	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:140675600-140692600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:140675600-140698200	Weak transcription	Pancreas	Pancrea
49	chr3:140675800-140684600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:140676200-140692800	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links