Variant report

Variant	rs10876135
Chromosome Location	chr12:51488236-51488237
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51483401..51485613-chr12:51487391..51490176,3	K562	blood:
2	chr12:51484035..51486422-chr12:51486833..51488800,2	MCF-7	breast:
3	chr12:51474025..51479149-chr12:51485745..51494502,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10876133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876137	0.90[ASN][1000 genomes]
rs10876142	0.84[ASN][1000 genomes]
rs1112391	0.86[YRI][hapmap]
rs11169658	0.83[CHB][hapmap]
rs11169696	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169700	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11169706	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11169708	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11169720	0.87[ASN][1000 genomes]
rs11169721	0.85[ASN][1000 genomes]
rs11169722	0.87[ASN][1000 genomes]
rs11169734	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs11169735	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11169737	0.81[ASN][1000 genomes]
rs11169747	0.94[JPT][hapmap]
rs11610454	0.81[ASN][1000 genomes]
rs11614806	0.80[ASN][1000 genomes]
rs12227032	0.87[ASN][1000 genomes]
rs12227973	0.86[ASN][1000 genomes]
rs12230388	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12312531	0.91[ASN][1000 genomes]
rs12424460	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs1493382	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17125363	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17125365	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17125371	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2018022	0.85[YRI][hapmap]
rs2359189	1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2436636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2452794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2452795	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2452796	0.86[ASN][1000 genomes]
rs2640512	0.86[ASN][1000 genomes]
rs2640515	0.86[ASN][1000 genomes]
rs2640518	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2640520	0.87[ASN][1000 genomes]
rs2640522	0.87[ASN][1000 genomes]
rs2640525	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs2640526	0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2640528	0.86[ASN][1000 genomes]
rs2730651	0.82[ASN][1000 genomes]
rs2730653	0.87[ASN][1000 genomes]
rs2730657	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2730659	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2934092	0.81[ASN][1000 genomes]
rs2956427	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2956433	0.80[ASN][1000 genomes]
rs4768953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768957	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs4768971	0.86[ASN][1000 genomes]
rs4768974	0.87[ASN][1000 genomes]
rs56729853	0.86[ASN][1000 genomes]
rs7309374	0.86[ASN][1000 genomes]
rs7310257	0.81[AMR][1000 genomes]
rs7399214	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs7953765	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7980076	0.82[ASN][1000 genomes]
rs8490	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[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
rs10876135	LETMD1	cis	lymphoblastoid	seeQTL
rs10876135	TFCP2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51477400-51488800	Weak transcription	Gastric	stomach
2	chr12:51477400-51490000	Weak transcription	Small Intestine	intestine
3	chr12:51477400-51518200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:51477800-51488400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:51477800-51488600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:51477800-51488800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:51477800-51490000	Weak transcription	Aorta	Aorta
8	chr12:51477800-51492600	Weak transcription	Esophagus	oesophagus
9	chr12:51477800-51499600	Weak transcription	NHLF	lung
10	chr12:51477800-51518400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:51477800-51518400	Weak transcription	Pancreas	Pancrea
12	chr12:51477800-51550200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:51478000-51496000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:51478200-51493200	Weak transcription	Fetal Brain Male	brain
15	chr12:51479800-51492000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:51482800-51498000	Strong transcription	Fetal Muscle Leg	muscle
17	chr12:51482800-51499400	Strong transcription	Fetal Stomach	stomach
18	chr12:51483000-51492200	Weak transcription	K562	blood
19	chr12:51483800-51513400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:51484000-51491000	Strong transcription	HSMM	muscle
21	chr12:51484000-51502000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr12:51484000-51519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr12:51484400-51506000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr12:51484800-51507000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:51485000-51498400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:51485000-51507600	Strong transcription	Duodenum Mucosa	Duodenum
27	chr12:51485000-51513200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:51485200-51493400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr12:51485600-51498200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr12:51485600-51498200	Strong transcription	Fetal Thymus	thymus
31	chr12:51485800-51497400	Strong transcription	Fetal Intestine Small	intestine
32	chr12:51485800-51513200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:51486000-51489400	Strong transcription	Lung	lung
34	chr12:51486000-51490600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:51486000-51490800	Strong transcription	GM12878-XiMat	blood
36	chr12:51486000-51511400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:51486400-51510800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:51486600-51508000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:51486800-51497800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:51486800-51504600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr12:51486800-51508000	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr12:51487000-51490800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:51487000-51498200	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr12:51487000-51505000	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:51487000-51506600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr12:51487000-51511400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr12:51487200-51498000	Strong transcription	Osteobl	bone
48	chr12:51487200-51498200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:51487200-51498400	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:51487200-51502000	Strong transcription	Primary monocytes fromperipheralblood	blood

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