Variant report

Variant	rs10195398
Chromosome Location	chr2:172272690-172272691
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:172009192..172011548-chr2:172270786..172273321,2	K562	blood:
2	chr2:172270914..172275149-chr2:172275462..172279658,6	K562	blood:
3	chr2:172015616..172017761-chr2:172271152..172272814,2	MCF-7	breast:
4	chr2:171829670..171830422-chr2:172272305..172273239,6	MCF-7	breast:
5	chr2:172271134..172274908-chr2:172289137..172291473,5	MCF-7	breast:
6	chr2:172269451..172273904-chr2:172275650..172277742,4	K562	blood:
7	chr2:172271657..172275800-chr2:172289994..172293745,6	K562	blood:
8	chr2:172017358..172018279-chr2:172272338..172273091,4	MCF-7	breast:
9	chr2:172020395..172022447-chr2:172272199..172274902,2	MCF-7	breast:
10	chr2:172271335..172273049-chr2:172276074..172277809,2	MCF-7	breast:
11	chr2:172267840..172270296-chr2:172270765..172273449,2	K562	blood:
12	chr2:172272617..172274293-chr2:172289198..172291820,2	K562	blood:
13	chr2:172015744..172019134-chr2:172270782..172274226,5	K562	blood:
14	chr2:172270978..172272997-chr2:172289315..172290964,3	MCF-7	breast:
15	chr2:172016348..172019248-chr2:172270460..172274931,6	MCF-7	breast:
16	chr2:172272632..172275850-chr2:172285670..172289133,3	K562	blood:
17	chr2:171829613..171830619-chr2:172272303..172273269,4	K562	blood:
18	chr2:172272632..172274572-chr2:172285670..172288180,2	K562	blood:
19	chr2:171829283..171832000-chr2:172272425..172274768,3	MCF-7	breast:
20	chr2:172271841..172274486-chr2:172281833..172284953,3	K562	blood:
21	chr2:171831104..171831914-chr2:172272322..172273272,2	K562	blood:
22	chr2:172016440..172019134-chr2:172272291..172274226,3	K562	blood:
23	chr2:171092275..171093118-chr2:172272365..172273194,2	K562	blood:
24	chr2:171830276..171832132-chr2:172271180..172272801,2	MCF-7	breast:
25	chr2:172267543..172269824-chr2:172270765..172273272,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000123600	Chromatin interaction
ENSG00000198586	Chromatin interaction
ENSG00000115827	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10173812	0.89[ASN][1000 genomes]
rs10192493	0.92[CHD][hapmap]
rs10202883	0.92[CHD][hapmap]
rs10210332	0.92[CHD][hapmap]
rs1125991	0.88[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12327994	0.85[CHD][hapmap]
rs13390534	0.89[ASW][hapmap];0.80[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13402901	0.92[CHD][hapmap]
rs13414723	0.92[CHD][hapmap]
rs3731986	0.85[CHD][hapmap]
rs4566333	0.92[CHD][hapmap]
rs60545517	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6709526	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6712098	0.92[CHD][hapmap]
rs7564847	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs888427	0.90[CHB][hapmap]
rs888521	0.85[CHD][hapmap]

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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172222200-172289600	Weak transcription	Gastric	stomach
2	chr2:172261600-172277800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:172266400-172277400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr2:172266400-172280400	Weak transcription	Esophagus	oesophagus
5	chr2:172266400-172280400	Weak transcription	Left Ventricle	heart
6	chr2:172266400-172289600	Weak transcription	Psoas Muscle	Psoas
7	chr2:172266400-172289600	Weak transcription	Right Ventricle	heart
8	chr2:172268800-172289200	Weak transcription	HSMM	muscle
9	chr2:172269000-172280400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:172269200-172280200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:172269600-172280400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:172269800-172273600	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:172271000-172274200	Enhancers	K562	blood
14	chr2:172271200-172272800	Enhancers	Primary B cells from peripheral blood	blood
15	chr2:172272200-172272800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:172272200-172272800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:172272200-172273000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr2:172272200-172273000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:172272200-172273000	Enhancers	Liver	Liver
20	chr2:172272200-172273000	Enhancers	Fetal Intestine Small	intestine
21	chr2:172272200-172273200	Enhancers	HepG2	liver
22	chr2:172272400-172272800	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr2:172272400-172272800	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr2:172272400-172272800	Enhancers	Primary T cells fromperipheralblood	blood
25	chr2:172272400-172272800	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr2:172272400-172272800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr2:172272400-172272800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:172272400-172272800	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr2:172272400-172272800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:172272400-172272800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr2:172272400-172272800	Enhancers	Fetal Lung	lung
32	chr2:172272400-172272800	Enhancers	Ovary	ovary
33	chr2:172272400-172272800	Enhancers	Stomach Mucosa	stomach
34	chr2:172272400-172273000	Enhancers	H1 Cell Line	embryonic stem cell
35	chr2:172272400-172273000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:172272400-172273000	Enhancers	Rectal Smooth Muscle	rectum
37	chr2:172272400-172273200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr2:172272400-172273200	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr2:172272400-172273200	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr2:172272400-172273200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:172272400-172273200	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr2:172272400-172273200	Enhancers	Brain Cingulate Gyrus	brain
43	chr2:172272400-172273400	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr2:172272400-172273400	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr2:172272600-172272800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:172272600-172272800	Weak transcription	Primary T cells from cord blood	blood
47	chr2:172272600-172272800	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr2:172272600-172272800	Active TSS	Fetal Kidney	kidney
49	chr2:172272600-172272800	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr2:172272600-172272800	Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links