Variant report

Variant	rs11610644
Chromosome Location	chr12:51487235-51487236
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51484035..51486422-chr12:51486833..51488800,2	MCF-7	breast:
2	chr12:51474025..51479149-chr12:51485745..51494502,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10275	0.88[EUR][1000 genomes]
rs10783413	0.91[ASN][1000 genomes]
rs10876127	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876128	0.88[EUR][1000 genomes]
rs10876129	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876130	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10876131	0.86[EUR][1000 genomes]
rs10876132	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10876136	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876138	0.94[ASN][1000 genomes]
rs10876139	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169695	0.88[EUR][1000 genomes]
rs11169707	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169710	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12370120	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12424509	0.80[ASN][1000 genomes]
rs12427345	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1466579	0.89[ASN][1000 genomes]
rs1486014	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs15756	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2029145	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2029146	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs224572	0.80[ASN][1000 genomes]
rs2730655	0.94[ASN][1000 genomes]
rs370462	0.80[ASN][1000 genomes]
rs427020	0.80[ASN][1000 genomes]
rs4438107	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55874804	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61934800	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6580782	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6580785	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580791	0.94[ASN][1000 genomes]
rs7135399	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7136960	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7953867	0.91[ASN][1000 genomes]
rs7958068	0.88[EUR][1000 genomes]
rs7969803	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7976431	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs901313	0.89[ASN][1000 genomes]
rs9739342	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11610644	LETMD1	Cis_1M	lymphoblastoid	RTeQTL
rs11610644	TFCP2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51477400-51488200	Weak transcription	Spleen	Spleen
2	chr12:51477400-51488800	Weak transcription	Gastric	stomach
3	chr12:51477400-51490000	Weak transcription	Small Intestine	intestine
4	chr12:51477400-51518200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:51477600-51487800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:51477800-51487400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:51477800-51487400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:51477800-51487400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:51477800-51487400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:51477800-51487400	Weak transcription	HMEC	breast
11	chr12:51477800-51487600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:51477800-51487600	Weak transcription	Primary T cells from cord blood	blood
13	chr12:51477800-51487600	Weak transcription	Adipose Nuclei	Adipose
14	chr12:51477800-51487600	Weak transcription	Brain Substantia Nigra	brain
15	chr12:51477800-51487600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:51477800-51487800	Weak transcription	Liver	Liver
17	chr12:51477800-51487800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:51477800-51487800	Weak transcription	Colon Smooth Muscle	Colon
19	chr12:51477800-51487800	Weak transcription	Left Ventricle	heart
20	chr12:51477800-51487800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:51477800-51487800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:51477800-51487800	Weak transcription	Hela-S3	cervix
23	chr12:51477800-51487800	Weak transcription	NH-A	brain
24	chr12:51477800-51487800	Weak transcription	NHDF-Ad	bronchial
25	chr12:51477800-51488000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:51477800-51488000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr12:51477800-51488000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:51477800-51488000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:51477800-51488000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr12:51477800-51488000	Weak transcription	Brain Angular Gyrus	brain
31	chr12:51477800-51488000	Weak transcription	Fetal Heart	heart
32	chr12:51477800-51488000	Weak transcription	Fetal Kidney	kidney
33	chr12:51477800-51488000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr12:51477800-51488000	Weak transcription	Thymus	Thymus
35	chr12:51477800-51488000	Weak transcription	HUVEC	blood vessel
36	chr12:51477800-51488000	Weak transcription	NHEK	skin
37	chr12:51477800-51488200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:51477800-51488200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:51477800-51488200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:51477800-51488200	Weak transcription	Ovary	ovary
41	chr12:51477800-51488200	Weak transcription	Right Ventricle	heart
42	chr12:51477800-51488400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr12:51477800-51488600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr12:51477800-51488800	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr12:51477800-51490000	Weak transcription	Aorta	Aorta
46	chr12:51477800-51492600	Weak transcription	Esophagus	oesophagus
47	chr12:51477800-51499600	Weak transcription	NHLF	lung
48	chr12:51477800-51518400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:51477800-51518400	Weak transcription	Pancreas	Pancrea
50	chr12:51477800-51550200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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