Variant report

Variant	rs2498968
Chromosome Location	chr1:62435141-62435142
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10889271	0.83[CHD][hapmap]
rs11207877	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs1815464	0.83[EUR][1000 genomes]
rs1888988	0.82[EUR][1000 genomes]
rs2151124	1.00[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2251182	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2365735	0.83[ASN][1000 genomes]
rs2482860	0.92[EUR][1000 genomes]
rs2482861	0.92[EUR][1000 genomes]
rs2482862	0.94[EUR][1000 genomes]
rs2482863	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2482865	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2482868	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2482881	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2482886	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2482888	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2482889	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2498954	0.81[CHB][hapmap]
rs2498955	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2498958	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2498962	0.90[CHB][hapmap];0.93[CHD][hapmap];0.93[YRI][hapmap];0.89[ASN][1000 genomes]
rs3737108	0.81[CHB][hapmap]
rs6668270	0.84[CHD][hapmap]
rs7512525	0.81[CHD][hapmap]
rs7530734	0.81[CHB][hapmap];0.87[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1110	chr1:62395723-62454435	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv546415	chr1:62405873-62437872	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
9	nsv437210	chr1:62419727-62448245	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv2753481	chr1:62424207-62478878	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1010655	chr1:62427826-62447302	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv3693433	chr1:62429665-62448451	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv1805048	chr1:62433100-62448451	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv1812337	chr1:62433100-62448451	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv1814392	chr1:62433100-62448451	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv1815127	chr1:62433100-62448451	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv1806702	chr1:62433100-62452173	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	esv1807506	chr1:62433100-62452173	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	esv1813605	chr1:62433814-62453540	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv10217	chr1:62433904-62453204	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2498968	INADL	cis	lymphoblastoid	seeQTL
rs2498968	EFCAB7	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62385000-62494200	Weak transcription	Aorta	Aorta
2	chr1:62409000-62436800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr1:62409200-62456000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:62409200-62456800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:62409200-62457000	Weak transcription	Fetal Intestine Large	intestine
6	chr1:62409200-62518600	Weak transcription	Pancreas	Pancrea
7	chr1:62409400-62458400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:62418200-62446400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:62418400-62441400	Weak transcription	Fetal Kidney	kidney
10	chr1:62419600-62445800	Weak transcription	Left Ventricle	heart
11	chr1:62424200-62436600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:62424200-62494200	Weak transcription	Esophagus	oesophagus
13	chr1:62424800-62438200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:62425000-62441400	Weak transcription	Stomach Mucosa	stomach
15	chr1:62430600-62435400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:62430600-62442200	Weak transcription	Fetal Intestine Small	intestine
17	chr1:62432000-62435600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:62432200-62439000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:62433400-62439200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:62433600-62456800	Weak transcription	NHEK	skin
21	chr1:62433800-62438600	Weak transcription	HMEC	breast
22	chr1:62433800-62444800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:62433800-62445400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:62434000-62457000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:62434800-62444800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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