Variant report

Variant	rs12630641
Chromosome Location	chr3:47534836-47534837
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47522323..47523883-chr3:47534294..47537270,2	MCF-7	breast:
2	chr3:47519490..47521448-chr3:47532935..47535413,2	K562	blood:
3	chr3:47527701..47530280-chr3:47534062..47536180,2	K562	blood:
4	chr3:47532827..47535628-chr3:47539625..47541232,2	K562	blood:
5	chr3:47534553..47536287-chr3:47537142..47539341,2	K562	blood:
6	chr3:47534428..47536854-chr3:47544325..47547166,3	K562	blood:
7	chr3:47534370..47536287-chr3:47537725..47539806,3	K562	blood:
8	chr3:47520594..47523805-chr3:47534550..47538420,3	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPN23-4	chr3:47534020-47534920	NONHSAT089509

No data

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1038394	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10865946	0.80[EUR][1000 genomes]
rs11130128	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130129	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130132	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130133	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11130137	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11705957	0.81[EUR][1000 genomes]
rs11707895	0.93[EUR][1000 genomes]
rs11711265	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11711824	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11712445	0.81[EUR][1000 genomes]
rs11713413	0.90[EUR][1000 genomes]
rs11716763	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11719877	0.81[EUR][1000 genomes]
rs11914795	0.84[EUR][1000 genomes]
rs11914913	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11914932	0.84[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11925823	0.80[EUR][1000 genomes]
rs12486969	0.80[EUR][1000 genomes]
rs12489046	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12490058	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12492433	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12495169	0.82[ASN][1000 genomes]
rs12497225	0.81[EUR][1000 genomes]
rs12632132	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12636851	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13059519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13064843	0.81[EUR][1000 genomes]
rs13075233	0.81[EUR][1000 genomes]
rs1531875	0.82[EUR][1000 genomes]
rs17784882	0.98[EUR][1000 genomes]
rs1872164	0.81[EUR][1000 genomes]
rs2062278	0.81[EUR][1000 genomes]
rs2101247	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2291298	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs34634681	0.92[EUR][1000 genomes]
rs3736177	0.82[EUR][1000 genomes]
rs3816779	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4599332	0.93[EUR][1000 genomes]
rs4858856	0.92[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4858868	0.82[EUR][1000 genomes]
rs4858894	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56032309	0.81[EUR][1000 genomes]
rs57346147	0.81[EUR][1000 genomes]
rs59586735	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60369822	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62248599	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62248603	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62248605	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62260710	0.95[EUR][1000 genomes]
rs62260711	0.95[EUR][1000 genomes]
rs62260741	0.90[EUR][1000 genomes]
rs6765990	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6787422	0.81[EUR][1000 genomes]
rs6790763	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6792461	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6792488	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6800271	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73081205	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7628631	0.98[EUR][1000 genomes]
rs7649234	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651194	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7651762	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs878659	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs922957	0.81[EUR][1000 genomes]
rs9683033	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9683177	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12630641	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs12630641	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47517800-47535200	Weak transcription	Esophagus	oesophagus
2	chr3:47517800-47536600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:47517800-47544400	Weak transcription	Small Intestine	intestine
4	chr3:47518200-47536600	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr3:47518200-47541600	Weak transcription	Fetal Kidney	kidney
6	chr3:47518400-47535200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:47518400-47535600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:47518400-47536600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:47518400-47536600	Weak transcription	Primary T cells from cord blood	blood
10	chr3:47518400-47536600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:47518400-47536600	Weak transcription	Aorta	Aorta
12	chr3:47518400-47536600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:47518400-47536600	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:47518400-47536600	Weak transcription	Gastric	stomach
15	chr3:47518400-47536600	Weak transcription	HSMMtube	muscle
16	chr3:47518400-47536600	Weak transcription	NHLF	lung
17	chr3:47518400-47536800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:47518400-47536800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:47518400-47537000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:47518400-47539400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:47518600-47535400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:47518600-47536400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:47518600-47536600	Weak transcription	Primary B cells from cord blood	blood
24	chr3:47518600-47536600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:47518600-47536600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:47518600-47536600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:47518600-47536600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:47518600-47536600	Weak transcription	Adipose Nuclei	Adipose
29	chr3:47518600-47536600	Weak transcription	Placenta	Placenta
30	chr3:47518600-47536600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:47518600-47536800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:47518600-47536800	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:47518600-47536800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:47518800-47535200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:47518800-47535200	Weak transcription	Liver	Liver
36	chr3:47518800-47535400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:47518800-47536600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:47518800-47536600	Weak transcription	Brain Anterior Caudate	brain
39	chr3:47518800-47536600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr3:47518800-47536600	Weak transcription	Pancreas	Pancrea
41	chr3:47518800-47536600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:47518800-47536600	Weak transcription	Spleen	Spleen
43	chr3:47518800-47536800	Weak transcription	Brain Angular Gyrus	brain
44	chr3:47518800-47536800	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:47518800-47536800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:47518800-47536800	Weak transcription	Right Ventricle	heart
47	chr3:47518800-47537000	Weak transcription	Fetal Lung	lung
48	chr3:47519600-47536600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr3:47522200-47536400	Weak transcription	HepG2	liver
50	chr3:47524000-47536600	Weak transcription	Ovary	ovary

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