Variant report

Variant	rs6714241
Chromosome Location	chr2:63069112-63069113
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10153716	0.88[ASN][1000 genomes]
rs1022110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11688816	0.85[CEU][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs11893131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12713469	0.98[LWK][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes]
rs13410889	0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.85[ASN][1000 genomes]
rs13418889	0.92[ASN][1000 genomes]
rs1468748	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17027429	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1828398	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1877026	0.87[CHD][hapmap]
rs2058567	0.96[ASN][1000 genomes]
rs2080227	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2421816	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2539978	0.89[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs2539980	0.84[ASW][hapmap];0.88[LWK][hapmap];0.86[YRI][hapmap]
rs2539982	0.83[ASN][1000 genomes]
rs2539984	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2710637	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2710639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2710641	0.86[AFR][1000 genomes]
rs34104251	0.85[ASN][1000 genomes]
rs4671051	0.90[ASN][1000 genomes]
rs4671448	0.86[YRI][hapmap]
rs6545972	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6545973	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6705798	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs7557501	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7562149	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7567923	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7571916	0.94[ASN][1000 genomes]
rs7591708	0.89[ASW][hapmap];0.88[CHD][hapmap];0.91[LWK][hapmap];0.89[YRI][hapmap]
rs9789661	0.91[ASN][1000 genomes]
rs9973612	1.00[JPT][hapmap]

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	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv428041	chr2:63027947-63206574	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6714241	SERTAD2	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63020600-63082000	Weak transcription	Pancreas	Pancrea
2	chr2:63031000-63083000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:63031400-63082000	Weak transcription	Thymus	Thymus
4	chr2:63040600-63082000	Weak transcription	Lung	lung
5	chr2:63045600-63072400	Weak transcription	NHEK	skin
6	chr2:63046400-63101800	Weak transcription	Brain Angular Gyrus	brain
7	chr2:63050600-63091800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:63052000-63099600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:63052200-63098200	Weak transcription	Hela-S3	cervix
10	chr2:63054600-63099800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:63054800-63091600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr2:63055000-63082000	Weak transcription	Esophagus	oesophagus
13	chr2:63056400-63081800	Weak transcription	NHLF	lung
14	chr2:63060800-63069400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:63060800-63081000	Weak transcription	Left Ventricle	heart
16	chr2:63060800-63081800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:63061000-63073000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:63061000-63073200	Weak transcription	NH-A	brain
19	chr2:63061000-63080400	Weak transcription	Aorta	Aorta
20	chr2:63061200-63071400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:63061200-63080800	Weak transcription	Psoas Muscle	Psoas
22	chr2:63061200-63115200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:63061400-63071200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:63061400-63071200	Weak transcription	Ovary	ovary
25	chr2:63061400-63080400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:63061400-63102000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:63061600-63071800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:63061600-63072600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:63061600-63082000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:63061800-63073200	Weak transcription	Primary B cells from cord blood	blood
31	chr2:63061800-63080800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr2:63062000-63070800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:63062000-63071400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:63062000-63071400	Weak transcription	Primary T cells from cord blood	blood
35	chr2:63062000-63071600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:63062000-63071800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:63062000-63071800	Weak transcription	HSMM	muscle
38	chr2:63062000-63072600	Weak transcription	Adipose Nuclei	Adipose
39	chr2:63062000-63073000	Weak transcription	Fetal Kidney	kidney
40	chr2:63062000-63073000	Weak transcription	Fetal Lung	lung
41	chr2:63062000-63076400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:63062000-63080600	Weak transcription	Brain Germinal Matrix	brain
43	chr2:63062000-63081200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:63062000-63082400	Weak transcription	HMEC	breast
45	chr2:63062000-63093000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr2:63062200-63071200	Weak transcription	A549	lung
47	chr2:63062200-63071400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:63062200-63071800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:63062200-63072800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:63062200-63073000	Weak transcription	Fetal Brain Female	brain

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