Variant report

Variant	rs12538826
Chromosome Location	chr7:99030228-99030229
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99028798..99032281-chr7:99034267..99038059,8	MCF-7	breast:
2	chr7:99007985..99010894-chr7:99027343..99030538,3	MCF-7	breast:
3	chr7:99004079..99005950-chr7:99029849..99032633,2	MCF-7	breast:
4	chr7:99026847..99029073-chr7:99029475..99031383,3	K562	blood:
5	chr7:99029730..99032537-chr7:99050314..99053165,2	MCF-7	breast:
6	chr7:99027922..99030424-chr7:99032965..99035110,3	K562	blood:
7	chr7:99014925..99017023-chr7:99029378..99031176,2	K562	blood:

Variant related genes	Relation type
ENSG00000106246	Chromatin interaction
ENSG00000160917	Chromatin interaction
ENSG00000106245	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10215854	0.86[EUR][1000 genomes]
rs10240199	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10244158	0.83[ASN][1000 genomes]
rs10264505	0.83[EUR][1000 genomes]
rs10265385	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10271049	0.87[ASN][1000 genomes]
rs1043466	0.82[ASN][1000 genomes]
rs10464604	0.99[ASN][1000 genomes]
rs10808112	0.86[EUR][1000 genomes]
rs11539770	0.99[ASN][1000 genomes]
rs11973173	0.86[EUR][1000 genomes]
rs12533251	0.81[EUR][1000 genomes]
rs13227522	0.86[EUR][1000 genomes]
rs13227795	0.82[ASN][1000 genomes]
rs13240600	0.82[ASN][1000 genomes]
rs13437771	0.82[ASN][1000 genomes]
rs17161768	0.85[ASN][1000 genomes]
rs17161769	0.85[ASN][1000 genomes]
rs1980307	0.82[ASN][1000 genomes]
rs2240384	0.87[ASN][1000 genomes]
rs2240385	0.99[ASN][1000 genomes]
rs2280600	0.82[ASN][1000 genomes]
rs2280601	0.82[ASN][1000 genomes]
rs28419687	0.81[EUR][1000 genomes]
rs28457808	0.81[ASN][1000 genomes]
rs28602855	0.86[EUR][1000 genomes]
rs28627543	0.86[EUR][1000 genomes]
rs34257469	0.81[EUR][1000 genomes]
rs3779354	0.81[ASN][1000 genomes]
rs3800960	0.85[ASN][1000 genomes]
rs45492098	0.95[ASN][1000 genomes]
rs45540134	0.94[ASN][1000 genomes]
rs45622743	0.98[ASN][1000 genomes]
rs58222677	0.92[ASN][1000 genomes]
rs60301933	0.86[ASN][1000 genomes]
rs61159815	0.93[ASN][1000 genomes]
rs61402640	0.89[ASN][1000 genomes]
rs61543997	0.89[ASN][1000 genomes]
rs66509940	0.84[EUR][1000 genomes]
rs6962772	0.83[ASN][1000 genomes]
rs72494451	0.85[ASN][1000 genomes]
rs72494452	0.85[ASN][1000 genomes]
rs7794682	0.87[ASN][1000 genomes]
rs7794705	0.84[ASN][1000 genomes]
rs883403	0.84[ASN][1000 genomes]
rs917154	0.81[ASN][1000 genomes]
rs940336	0.99[ASN][1000 genomes]
rs9632722	0.81[EUR][1000 genomes]
rs9656060	0.81[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	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv888767	chr7:99017832-99050039	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv888768	chr7:99017832-99052428	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv888769	chr7:99018584-99041748	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
6	nsv888770	chr7:99021344-99041748	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12538826	ARPC1B	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99007200-99035400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:99011400-99035000	Weak transcription	Fetal Brain Male	brain
3	chr7:99011600-99032200	Weak transcription	NHDF-Ad	bronchial
4	chr7:99015600-99035200	Weak transcription	Fetal Kidney	kidney
5	chr7:99015600-99035400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:99015600-99035600	Weak transcription	Stomach Mucosa	stomach
7	chr7:99016800-99036000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:99017600-99035600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:99018200-99035200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:99018200-99035400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:99018400-99035600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr7:99021400-99034400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:99021600-99035200	Weak transcription	HMEC	breast
14	chr7:99022200-99035400	Weak transcription	NH-A	brain
15	chr7:99023000-99036000	Weak transcription	Small Intestine	intestine
16	chr7:99025600-99031400	Strong transcription	Primary B cells from peripheral blood	blood
17	chr7:99025600-99033000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:99025600-99033000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr7:99025600-99033000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr7:99025600-99033000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr7:99025600-99033200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:99025600-99033200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr7:99025600-99033400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:99025600-99033400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:99025600-99033800	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr7:99025600-99034400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:99025600-99034800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:99025600-99034800	Strong transcription	Fetal Muscle Leg	muscle
29	chr7:99025600-99035200	Strong transcription	Fetal Stomach	stomach
30	chr7:99025800-99031200	Strong transcription	Thymus	Thymus
31	chr7:99025800-99033000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr7:99025800-99033200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr7:99025800-99034000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr7:99026000-99032800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr7:99026000-99032800	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr7:99026000-99033200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr7:99026200-99031400	Strong transcription	Brain Anterior Caudate	brain
38	chr7:99026200-99032400	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr7:99026200-99032800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr7:99026200-99032800	Strong transcription	Colonic Mucosa	Colon
41	chr7:99026200-99032800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr7:99026200-99032800	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr7:99026200-99032800	Strong transcription	Fetal Brain Female	brain
44	chr7:99026200-99032800	Strong transcription	Fetal Thymus	thymus
45	chr7:99026200-99032800	Strong transcription	Stomach Smooth Muscle	stomach
46	chr7:99026200-99033000	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr7:99026200-99033000	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr7:99026200-99033000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr7:99026200-99033000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr7:99026200-99033000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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