Variant report

Variant	rs2482881
Chromosome Location	chr1:62424007-62424008
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62420887..62422924-chr1:62423218..62424749,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10889271	0.82[CHB][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs10889272	0.82[CHB][hapmap];0.86[CHD][hapmap];0.88[ASN][1000 genomes]
rs10889277	0.82[CHB][hapmap]
rs10889278	0.88[ASN][1000 genomes]
rs10889279	0.88[ASN][1000 genomes]
rs11207869	0.88[ASN][1000 genomes]
rs11207877	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs11207878	0.82[ASN][1000 genomes]
rs1815464	0.81[EUR][1000 genomes]
rs2151124	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2365735	0.90[ASN][1000 genomes]
rs2482860	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2482861	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2482862	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2482863	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2482865	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2482868	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2482886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2482888	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2482889	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2498954	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs2498955	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2498958	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2498962	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs2498968	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]
rs3737108	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs6587949	0.82[CHB][hapmap]
rs6668270	0.82[CHB][hapmap];0.90[CHD][hapmap];0.80[ASN][1000 genomes]
rs6698695	0.82[CHB][hapmap]
rs7512525	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs7530734	0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1011842	chr1:62414911-62428530	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2482881	INADL	cis	lymphoblastoid	seeQTL
rs2482881	HOOK1	cis	parietal	SCAN
rs2482881	EFCAB7	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62350600-62428200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:62385000-62494200	Weak transcription	Aorta	Aorta
3	chr1:62406600-62430200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:62409000-62436800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr1:62409200-62456000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:62409200-62456800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:62409200-62457000	Weak transcription	Fetal Intestine Large	intestine
8	chr1:62409200-62518600	Weak transcription	Pancreas	Pancrea
9	chr1:62409400-62429600	Weak transcription	Gastric	stomach
10	chr1:62409400-62458400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:62410200-62425200	Weak transcription	Fetal Intestine Small	intestine
12	chr1:62416800-62426800	Weak transcription	HepG2	liver
13	chr1:62417800-62431600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:62418000-62428800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:62418200-62446400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:62418400-62441400	Weak transcription	Fetal Kidney	kidney
17	chr1:62418600-62432400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:62418600-62432400	Weak transcription	NHEK	skin
19	chr1:62418800-62432800	Weak transcription	HMEC	breast
20	chr1:62419200-62424400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:62419600-62426800	Weak transcription	Right Atrium	heart
22	chr1:62419600-62445800	Weak transcription	Left Ventricle	heart
23	chr1:62420800-62429800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr1:62421200-62424200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:62422800-62432600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:62423400-62431200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:62423400-62433600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:62423600-62433800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:62423800-62432800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:62424000-62432000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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