Variant report

Variant	rs12629262
Chromosome Location	chr3:47196580-47196581
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47195998..47198423-chr3:47353673..47355758,2	K562	blood:
2	chr3:47184671..47186867-chr3:47196509..47199504,2	MCF-7	breast:
3	chr3:47193971..47196675-chr3:47199347..47201120,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11130114	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130115	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11708451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11712716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11714282	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11714373	0.90[EUR][1000 genomes]
rs11716539	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11718795	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11719306	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11719738	0.91[EUR][1000 genomes]
rs11923706	0.85[EUR][1000 genomes]
rs12488225	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12489211	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12493425	0.91[EUR][1000 genomes]
rs12635619	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13061071	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13062022	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13063250	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13078131	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13084117	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13091054	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13094438	0.83[ASN][1000 genomes]
rs13094672	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13098228	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1466740	0.84[EUR][1000 genomes]
rs1466741	0.84[EUR][1000 genomes]
rs1811652	0.91[EUR][1000 genomes]
rs2132173	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2276853	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2276854	0.83[ASN][1000 genomes]
rs34103310	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4018905	0.88[EUR][1000 genomes]
rs4078466	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4082155	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4682852	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683320	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683322	0.80[EUR][1000 genomes]
rs4683324	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57756484	0.87[EUR][1000 genomes]
rs58956475	0.90[EUR][1000 genomes]
rs62246451	0.91[EUR][1000 genomes]
rs62246455	0.88[EUR][1000 genomes]
rs6414435	0.80[EUR][1000 genomes]
rs6414436	0.84[EUR][1000 genomes]
rs6442055	0.80[EUR][1000 genomes]
rs6442059	0.91[EUR][1000 genomes]
rs6763236	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6766230	0.91[EUR][1000 genomes]
rs6767907	0.90[EUR][1000 genomes]
rs6772670	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6773521	0.88[EUR][1000 genomes]
rs6777145	0.80[EUR][1000 genomes]
rs6781941	0.86[EUR][1000 genomes]
rs6785790	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6791062	0.89[EUR][1000 genomes]
rs6791842	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6794193	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7610636	0.81[EUR][1000 genomes]
rs7615323	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7620997	0.81[EUR][1000 genomes]
rs7621911	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7625067	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7625070	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9311403	0.87[EUR][1000 genomes]
rs9812878	0.81[EUR][1000 genomes]
rs9818382	0.91[EUR][1000 genomes]
rs9821119	0.91[EUR][1000 genomes]
rs9837343	0.91[EUR][1000 genomes]
rs9843075	0.87[EUR][1000 genomes]
rs9854790	0.80[EUR][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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv590210	chr3:47126543-47214122	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv590211	chr3:47189485-47256057	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12629262	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs12629262	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47165800-47197000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:47166000-47200800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:47166000-47201200	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:47166000-47204600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:47166200-47197200	Weak transcription	Aorta	Aorta
6	chr3:47166200-47200600	Weak transcription	Hela-S3	cervix
7	chr3:47166600-47204200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:47167400-47202400	Weak transcription	HSMM	muscle
9	chr3:47175800-47200400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:47182600-47200800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:47182800-47198200	Weak transcription	Primary B cells from cord blood	blood
12	chr3:47183600-47200800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:47183600-47202200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:47183800-47198000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:47183800-47202200	Weak transcription	NHEK	skin
16	chr3:47183800-47203000	Weak transcription	Colonic Mucosa	Colon
17	chr3:47184000-47197000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:47184400-47198400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:47184600-47198000	Weak transcription	Thymus	Thymus
20	chr3:47184600-47202200	Weak transcription	Esophagus	oesophagus
21	chr3:47184800-47197000	Weak transcription	Gastric	stomach
22	chr3:47184800-47199600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr3:47184800-47199800	Weak transcription	Fetal Intestine Small	intestine
24	chr3:47186800-47197000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:47187400-47197200	Weak transcription	Right Atrium	heart
26	chr3:47188400-47200800	Weak transcription	Fetal Stomach	stomach
27	chr3:47188600-47202000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:47190000-47200400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr3:47191200-47198000	Weak transcription	Right Ventricle	heart
30	chr3:47191200-47198000	Weak transcription	Small Intestine	intestine
31	chr3:47191200-47200600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:47191200-47202800	Weak transcription	HMEC	breast
33	chr3:47191400-47198000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:47191400-47201000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:47192000-47197000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:47192200-47197400	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:47192200-47198000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:47192200-47200400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:47192200-47202000	Weak transcription	Fetal Lung	lung
40	chr3:47192400-47198400	Weak transcription	Stomach Mucosa	stomach
41	chr3:47193400-47198000	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr3:47193400-47198400	Weak transcription	Lung	lung
43	chr3:47194000-47200800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:47194200-47200400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr3:47194400-47197000	Weak transcription	Adipose Nuclei	Adipose
46	chr3:47194400-47197600	Weak transcription	Osteobl	bone
47	chr3:47194400-47197800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr3:47194400-47197800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:47194400-47198400	Weak transcription	Ovary	ovary
50	chr3:47194400-47200600	Weak transcription	Fetal Heart	heart

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