Variant report

Variant	rs512421
Chromosome Location	chr11:65985168-65985169
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65983052..65986048-chr11:65987938..65993154,6	K562	blood:
2	chr11:65983181..65985305-chr11:65986434..65989438,4	K562	blood:
3	chr11:65985101..65987489-chr11:65988422..65991212,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175115	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10750777	0.85[ASN][1000 genomes]
rs10750778	0.92[ASN][1000 genomes]
rs10750780	0.88[ASN][1000 genomes]
rs10750781	0.96[ASN][1000 genomes]
rs10791849	0.87[ASN][1000 genomes]
rs10791850	0.94[ASN][1000 genomes]
rs10791851	0.94[ASN][1000 genomes]
rs10791852	0.94[ASN][1000 genomes]
rs10791854	0.97[ASN][1000 genomes]
rs10791855	0.97[ASN][1000 genomes]
rs10791858	0.99[ASN][1000 genomes]
rs10791859	0.99[ASN][1000 genomes]
rs10791860	0.97[ASN][1000 genomes]
rs10791861	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10791862	0.95[ASN][1000 genomes]
rs10791863	0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10896077	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10896080	0.87[ASN][1000 genomes]
rs10896081	0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10896085	0.89[ASN][1000 genomes]
rs10896087	0.89[ASN][1000 genomes]
rs10896089	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10896090	0.94[ASN][1000 genomes]
rs10896091	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10896093	0.95[ASN][1000 genomes]
rs10896094	0.95[ASN][1000 genomes]
rs10896098	0.96[ASN][1000 genomes]
rs10896099	0.97[ASN][1000 genomes]
rs10896100	0.97[ASN][1000 genomes]
rs10896105	0.96[ASN][1000 genomes]
rs11227403	0.82[ASN][1000 genomes]
rs11227409	0.87[ASN][1000 genomes]
rs11227410	0.87[ASN][1000 genomes]
rs11227411	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11227413	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11227414	0.86[ASN][1000 genomes]
rs11227415	0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11227420	0.94[ASN][1000 genomes]
rs11227433	0.99[ASN][1000 genomes]
rs11227439	0.94[ASN][1000 genomes]
rs11227447	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11227448	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11227452	0.90[ASN][1000 genomes]
rs11607393	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12797158	0.97[ASN][1000 genomes]
rs12797586	0.88[ASN][1000 genomes]
rs12800670	0.97[ASN][1000 genomes]
rs1862005	0.83[ASN][1000 genomes]
rs2017969	0.95[ASN][1000 genomes]
rs2155030	0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2155031	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2155198	0.99[ASN][1000 genomes]
rs2155201	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2177053	0.97[ASN][1000 genomes]
rs2177054	0.94[ASN][1000 genomes]
rs2236651	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2236652	0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2276036	0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs2282568	0.89[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs2293121	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2298466	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298468	0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2889313	0.97[ASN][1000 genomes]
rs3132851	0.81[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs3814738	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3825067	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3862386	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3953856	0.97[ASN][1000 genomes]
rs4013917	0.89[ASN][1000 genomes]
rs4393319	0.99[ASN][1000 genomes]
rs4483592	0.99[ASN][1000 genomes]
rs476551	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs535395	0.82[GIH][hapmap]
rs560393	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6591207	0.94[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6591208	0.94[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7120326	0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs7124165	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7925123	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7926402	0.87[ASN][1000 genomes]
rs7929909	0.94[ASN][1000 genomes]
rs7931477	0.89[ASN][1000 genomes]
rs7931544	0.89[ASN][1000 genomes]
rs7935336	0.87[ASN][1000 genomes]
rs7941431	0.96[ASN][1000 genomes]
rs7941469	0.82[GIH][hapmap]
rs7943911	0.94[ASN][1000 genomes]
rs7945723	0.96[ASN][1000 genomes]
rs7946917	0.84[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs7951079	0.97[ASN][1000 genomes]
rs918299	0.89[ASN][1000 genomes]
rs9645684	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9736673	0.89[ASN][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	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs512421	ROM1	cis	parietal	SCAN
rs512421	AHNAK	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65958800-65989200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:65959200-65989400	Weak transcription	K562	blood
3	chr11:65961400-66011200	Weak transcription	Psoas Muscle	Psoas
4	chr11:65964000-65989600	Weak transcription	Stomach Mucosa	stomach
5	chr11:65976400-65989200	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr11:65976400-65989600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr11:65976600-66006000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:65976800-65989600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr11:65976800-65996000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:65977000-65989800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr11:65977200-65996000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr11:65977400-65990000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:65977400-66010600	Strong transcription	Fetal Stomach	stomach
14	chr11:65977600-65985200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:65977600-65989400	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr11:65977600-65989400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr11:65977600-65989600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr11:65977600-65989800	Strong transcription	Fetal Intestine Small	intestine
19	chr11:65977600-66018600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr11:65977800-65985200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:65977800-65987800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:65977800-65987800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:65977800-65988800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:65977800-65988800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:65977800-65988800	Strong transcription	Lung	lung
26	chr11:65977800-65989400	Strong transcription	Adipose Nuclei	Adipose
27	chr11:65977800-65989800	Strong transcription	Primary T cells from cord blood	blood
28	chr11:65977800-65990000	Strong transcription	Fetal Muscle Leg	muscle
29	chr11:65978000-65989200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr11:65978000-65989400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:65978000-65989800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:65978000-65993000	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr11:65978800-65985400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr11:65978800-65989800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr11:65979600-65987000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr11:65979600-65989800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr11:65979800-66001200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr11:65980000-65994000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr11:65980400-65989200	Strong transcription	Primary B cells from cord blood	blood
40	chr11:65980600-65988400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr11:65980600-65988600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr11:65980600-65988800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:65981200-65990200	Weak transcription	Fetal Kidney	kidney
44	chr11:65982000-65988800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr11:65982000-65989000	Strong transcription	Esophagus	oesophagus
46	chr11:65982200-65989000	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr11:65982200-65995800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr11:65982400-65989000	Strong transcription	Osteobl	bone
49	chr11:65982600-65989200	Strong transcription	A549	lung
50	chr11:65982800-65985200	Strong transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links