Variant report

Variant	rs10876136
Chromosome Location	chr12:51490364-51490365
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51475858..51478802-chr12:51488243..51491629,4	K562	blood:
2	chr12:51474025..51479149-chr12:51485745..51494502,15	MCF-7	breast:
3	chr12:51480017..51482806-chr12:51490046..51492901,2	K562	blood:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10275	0.95[EUR][1000 genomes]
rs10783409	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10783413	0.89[ASN][1000 genomes]
rs10876127	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10876128	0.96[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs10876129	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10876130	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10876131	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10876132	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10876138	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs10876139	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169657	0.83[EUR][1000 genomes]
rs11169695	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11169707	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169710	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610644	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12370120	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12379	1.00[CHB][hapmap]
rs12424509	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs12427345	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1466579	0.87[ASN][1000 genomes]
rs1486014	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs15756	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1632791	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs17125111	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs17125340	0.82[JPT][hapmap]
rs2029145	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2029146	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs224448	0.83[EUR][1000 genomes]
rs224572	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs224575	0.81[CEU][hapmap]
rs2730655	0.96[ASN][1000 genomes]
rs319936	0.81[CEU][hapmap]
rs319939	0.81[CEU][hapmap]
rs370462	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs3759405	1.00[CHB][hapmap]
rs427020	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs4438107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55874804	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61934800	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6580782	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6580785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6580791	0.80[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs706805	0.82[EUR][1000 genomes]
rs7135399	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7136960	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7953867	1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs7958068	0.95[EUR][1000 genomes]
rs7961626	0.82[EUR][1000 genomes]
rs7969803	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971308	1.00[CHB][hapmap]
rs7976431	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7977740	0.81[EUR][1000 genomes]
rs901313	0.87[ASN][1000 genomes]
rs9739342	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[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
rs10876136	LETMD1	Cis_1M	lymphoblastoid	RTeQTL
rs10876136	DDN	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51477400-51518200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51477800-51492600	Weak transcription	Esophagus	oesophagus
3	chr12:51477800-51499600	Weak transcription	NHLF	lung
4	chr12:51477800-51518400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:51477800-51518400	Weak transcription	Pancreas	Pancrea
6	chr12:51477800-51550200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:51478000-51496000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:51478200-51493200	Weak transcription	Fetal Brain Male	brain
9	chr12:51479800-51492000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:51482800-51498000	Strong transcription	Fetal Muscle Leg	muscle
11	chr12:51482800-51499400	Strong transcription	Fetal Stomach	stomach
12	chr12:51483000-51492200	Weak transcription	K562	blood
13	chr12:51483800-51513400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:51484000-51491000	Strong transcription	HSMM	muscle
15	chr12:51484000-51502000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr12:51484000-51519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr12:51484400-51506000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:51484800-51507000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:51485000-51498400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:51485000-51507600	Strong transcription	Duodenum Mucosa	Duodenum
21	chr12:51485000-51513200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:51485200-51493400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:51485600-51498200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr12:51485600-51498200	Strong transcription	Fetal Thymus	thymus
25	chr12:51485800-51497400	Strong transcription	Fetal Intestine Small	intestine
26	chr12:51485800-51513200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:51486000-51490600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:51486000-51490800	Strong transcription	GM12878-XiMat	blood
29	chr12:51486000-51511400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:51486400-51510800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:51486600-51508000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:51486800-51497800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:51486800-51504600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:51486800-51508000	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr12:51487000-51490800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:51487000-51498200	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr12:51487000-51505000	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr12:51487000-51506600	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:51487000-51511400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr12:51487200-51498000	Strong transcription	Osteobl	bone
41	chr12:51487200-51498200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:51487200-51498400	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr12:51487200-51502000	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr12:51487200-51505000	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr12:51487200-51508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr12:51487200-51513000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr12:51487200-51513200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:51487400-51490400	Strong transcription	Primary hematopoietic stem cells	blood
49	chr12:51487400-51490400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
50	chr12:51487400-51490400	Strong transcription	HMEC	breast

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