Variant report

Variant	rs12540022
Chromosome Location	chr7:105197889-105197890
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:105197284..105199912-chr7:105208394..105210146,2	MCF-7	breast:
2	chr7:105170515..105175315-chr7:105197117..105202532,9	K562	blood:
3	chr7:105195414..105199100-chr7:105207061..105211736,4	K562	blood:
4	chr7:105172164..105175315-chr7:105195913..105199039,4	K562	blood:

Variant related genes	Relation type
ENSG00000223886	Chromatin interaction
ENSG00000272604	Chromatin interaction
ENSG00000135249	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12538052	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[EUR][1000 genomes]
rs1706888	0.84[JPT][hapmap]
rs1706914	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1706915	0.91[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs1728646	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1728649	0.92[JPT][hapmap]
rs1918875	0.92[JPT][hapmap]
rs2463632	0.85[EUR][1000 genomes]
rs2463634	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2689976	0.85[AFR][1000 genomes]
rs2692428	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2697019	0.88[ASN][1000 genomes]
rs4585682	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[EUR][1000 genomes]
rs55807006	0.81[EUR][1000 genomes]
rs62486981	0.85[EUR][1000 genomes]
rs62486982	0.84[EUR][1000 genomes]
rs62486983	0.89[EUR][1000 genomes]
rs62486989	0.90[EUR][1000 genomes]
rs62486990	0.90[EUR][1000 genomes]
rs62486991	0.90[EUR][1000 genomes]
rs62486992	0.90[EUR][1000 genomes]
rs62486993	0.90[EUR][1000 genomes]
rs62486996	0.90[EUR][1000 genomes]
rs62486997	0.90[EUR][1000 genomes]
rs62486998	0.90[EUR][1000 genomes]
rs62487001	0.87[EUR][1000 genomes]
rs67661063	0.86[ASN][1000 genomes]
rs6958132	0.84[CHB][hapmap]
rs698191	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs711427	0.91[JPT][hapmap]
rs711433	0.91[JPT][hapmap]
rs711434	0.81[ASN][1000 genomes]
rs711435	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7790660	0.89[EUR][1000 genomes]
rs7790913	0.89[EUR][1000 genomes]
rs818470	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs818479	0.85[EUR][1000 genomes]
rs818625	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9641352	1.00[CEU][hapmap]

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	esv2757233	chr7:104758250-105208492	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2759549	chr7:104758250-105208492	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv464668	chr7:105088693-105208492	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv608069	chr7:105088693-105208492	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:105173400-105208200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:105173400-105210200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:105174000-105204200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:105174000-105210200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:105174000-105212200	Weak transcription	Fetal Heart	heart
6	chr7:105174200-105210200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:105174200-105213800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:105174600-105210400	Weak transcription	Psoas Muscle	Psoas
9	chr7:105174600-105213200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr7:105174800-105209200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr7:105175000-105210400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:105175400-105201200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr7:105175400-105211000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:105175600-105209600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr7:105176000-105208600	Strong transcription	Placenta	Placenta
16	chr7:105176000-105210000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr7:105176000-105210200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:105176000-105210400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr7:105176000-105210400	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr7:105176200-105199800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:105176200-105210400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr7:105176200-105210400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr7:105176400-105209200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr7:105176600-105210200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr7:105176800-105198200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr7:105176800-105210400	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr7:105177000-105209200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr7:105177000-105210200	Strong transcription	Liver	Liver
29	chr7:105177200-105209400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr7:105177800-105202200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr7:105183600-105211000	Weak transcription	Small Intestine	intestine
32	chr7:105184200-105204400	Weak transcription	Fetal Brain Male	brain
33	chr7:105186400-105206600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr7:105186400-105210400	Strong transcription	Adipose Nuclei	Adipose
35	chr7:105187800-105210800	Weak transcription	Stomach Mucosa	stomach
36	chr7:105188000-105214200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr7:105189800-105199200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr7:105190200-105199400	Strong transcription	Dnd41	blood
39	chr7:105190400-105200800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:105191000-105208200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr7:105191000-105210200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr7:105191800-105207600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr7:105192200-105205800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr7:105192600-105200000	Weak transcription	HepG2	liver
45	chr7:105193000-105198800	Weak transcription	Brain Substantia Nigra	brain
46	chr7:105193000-105200400	Weak transcription	Brain Angular Gyrus	brain
47	chr7:105193000-105202400	Weak transcription	Fetal Kidney	kidney
48	chr7:105193000-105204600	Weak transcription	Gastric	stomach
49	chr7:105193000-105208200	Weak transcription	Right Ventricle	heart
50	chr7:105193200-105198400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links