Variant report

Variant	rs9862370
Chromosome Location	chr3:99576996-99576997
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99574432..99577221-chr3:99578950..99581441,2	K562	blood:
2	chr3:99574024..99577676-chr3:99581622..99586745,5	K562	blood:
3	chr3:99565953..99568570-chr3:99576514..99579322,2	MCF-7	breast:
4	chr3:99575686..99577216-chr3:99595048..99597854,2	K562	blood:
5	chr3:99575233..99577676-chr3:99581601..99584216,3	K562	blood:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12330310	1.00[AFR][1000 genomes]
rs13315221	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs13320602	1.00[YRI][hapmap]
rs13323384	1.00[AFR][1000 genomes]
rs13327351	0.83[AFR][1000 genomes]
rs13353487	1.00[AFR][1000 genomes]
rs16841800	1.00[AFR][1000 genomes]
rs16841824	1.00[AFR][1000 genomes]
rs16841828	0.83[AFR][1000 genomes]
rs16841836	1.00[AFR][1000 genomes]
rs16846956	0.83[AFR][1000 genomes]
rs28368726	1.00[AFR][1000 genomes]
rs28411225	0.83[AFR][1000 genomes]
rs28463921	1.00[AFR][1000 genomes]
rs28508384	1.00[AFR][1000 genomes]
rs28728176	0.83[AFR][1000 genomes]
rs28816814	1.00[AFR][1000 genomes]
rs9809706	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9810553	1.00[AFR][1000 genomes]
rs9816232	1.00[AFR][1000 genomes]
rs9820799	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9824229	1.00[AFR][1000 genomes]
rs9825382	1.00[AFR][1000 genomes]
rs9825938	1.00[AFR][1000 genomes]
rs9828782	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9830038	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9831309	1.00[YRI][hapmap]
rs9831706	0.83[AFR][1000 genomes]
rs9833005	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9835048	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9837028	1.00[AFR][1000 genomes]
rs9837204	1.00[AFR][1000 genomes]
rs9837555	1.00[AFR][1000 genomes]
rs9841053	1.00[AFR][1000 genomes]
rs9841758	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9843919	1.00[AFR][1000 genomes]
rs9844578	1.00[AFR][1000 genomes]
rs9844595	1.00[AFR][1000 genomes]
rs9849336	1.00[AFR][1000 genomes]
rs9849373	1.00[AFR][1000 genomes]
rs9851406	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9851985	0.83[AFR][1000 genomes]
rs9852857	1.00[AFR][1000 genomes]
rs9860986	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9868303	1.00[AFR][1000 genomes]
rs9870153	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9871500	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9875301	1.00[AFR][1000 genomes]
rs9883235	1.00[YRI][hapmap];1.00[AFR][1000 genomes]

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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
2	chr3:99538200-99584600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99559000-99578000	Weak transcription	HMEC	breast
4	chr3:99562200-99578000	Weak transcription	NHEK	skin
5	chr3:99562600-99578200	Weak transcription	Fetal Kidney	kidney
6	chr3:99562800-99580200	Weak transcription	Gastric	stomach
7	chr3:99563000-99577600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:99563200-99593600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:99564200-99577600	Weak transcription	Primary B cells from cord blood	blood
10	chr3:99565200-99585000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:99565400-99577600	Weak transcription	Fetal Heart	heart
12	chr3:99565600-99584800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:99565600-99589400	Weak transcription	K562	blood
14	chr3:99566000-99578400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:99567800-99581600	Weak transcription	Spleen	Spleen
16	chr3:99568000-99578600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:99568000-99580000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:99568600-99577600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:99569000-99589600	Weak transcription	Colonic Mucosa	Colon
20	chr3:99569800-99579200	Weak transcription	Right Ventricle	heart
21	chr3:99569800-99579400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:99569800-99580200	Weak transcription	Lung	lung
23	chr3:99570000-99577600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:99570400-99579200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:99570400-99579200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:99570600-99581600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:99570800-99577400	Weak transcription	Fetal Intestine Large	intestine
28	chr3:99571000-99579200	Enhancers	Rectal Smooth Muscle	rectum
29	chr3:99571000-99579400	Enhancers	Colon Smooth Muscle	Colon
30	chr3:99572600-99578000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:99572800-99577000	Strong transcription	Adipose Nuclei	Adipose
32	chr3:99573000-99580400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:99573200-99577400	Weak transcription	HSMMtube	muscle
34	chr3:99573200-99594000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:99573400-99589200	Genic enhancers	HepG2	liver
36	chr3:99573600-99584800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr3:99573800-99578000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:99574000-99579400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:99574000-99584000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:99574200-99578800	Weak transcription	Fetal Intestine Small	intestine
41	chr3:99574400-99577600	Weak transcription	Fetal Lung	lung
42	chr3:99574400-99577800	Strong transcription	HUVEC	blood vessel
43	chr3:99574400-99590000	Weak transcription	Liver	Liver
44	chr3:99574800-99577000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:99574800-99578200	Enhancers	Muscle Satellite Cultured Cells	--
46	chr3:99575000-99577600	Weak transcription	Fetal Stomach	stomach
47	chr3:99575000-99580200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:99575000-99587000	Weak transcription	Pancreas	Pancrea
49	chr3:99575000-99593600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:99575200-99578000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links