Variant report

Variant	rs7530734
Chromosome Location	chr1:62408549-62408550
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10889271	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10889272	0.91[CHB][hapmap];0.93[CHD][hapmap];0.92[ASN][1000 genomes]
rs10889277	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10889278	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10889279	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11207864	0.81[CHB][hapmap]
rs11207869	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11207877	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11207878	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12135923	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2151124	0.90[CHB][hapmap];0.87[CHD][hapmap];0.85[ASN][1000 genomes]
rs2251182	0.90[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs2482868	0.86[ASN][1000 genomes]
rs2482881	0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs2482886	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs2482889	0.85[ASN][1000 genomes]
rs2498954	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2498955	0.81[CHB][hapmap];0.86[ASN][1000 genomes]
rs2498958	0.86[ASN][1000 genomes]
rs2498962	0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs2498968	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs35506226	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3737108	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61775620	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6587949	0.91[CHB][hapmap]
rs6668270	0.91[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs6698695	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs7512525	0.81[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7530734	HOOK1	cis	parietal	SCAN
rs7530734	DAB1	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62336000-62408600	Weak transcription	Pancreas	Pancrea
2	chr1:62346200-62417600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:62350600-62428200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:62350800-62417600	Weak transcription	Ovary	ovary
5	chr1:62353800-62408800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:62361600-62408800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:62362000-62408600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:62372400-62408800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:62372400-62417600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:62374600-62410600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:62376200-62417600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:62380600-62408600	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:62380800-62410000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:62381000-62416000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:62381200-62417400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:62381200-62418400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:62384600-62408800	Weak transcription	Fetal Intestine Large	intestine
18	chr1:62385000-62494200	Weak transcription	Aorta	Aorta
19	chr1:62385400-62408600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:62386000-62408600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:62391800-62409000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:62392000-62408800	Weak transcription	Gastric	stomach
23	chr1:62392600-62408600	Weak transcription	Stomach Mucosa	stomach
24	chr1:62392600-62408800	Weak transcription	Left Ventricle	heart
25	chr1:62393800-62422400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:62395000-62408600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:62395000-62410800	Weak transcription	Liver	Liver
28	chr1:62396200-62408600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:62396200-62416000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:62396200-62417200	Weak transcription	HMEC	breast
31	chr1:62396400-62408600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:62396400-62418000	Weak transcription	Fetal Kidney	kidney
33	chr1:62397600-62408600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:62398200-62408600	Weak transcription	Esophagus	oesophagus
35	chr1:62398800-62408600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:62400600-62417600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:62401400-62408800	Weak transcription	Lung	lung
38	chr1:62406000-62408800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:62406600-62430200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:62407000-62409600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:62407200-62417400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:62408000-62409200	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:62408000-62409200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:62408200-62408600	Strong transcription	Fetal Intestine Small	intestine
45	chr1:62408200-62408600	Weak transcription	Fetal Stomach	stomach
46	chr1:62408200-62408600	Strong transcription	NHEK	skin
47	chr1:62408200-62408800	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:62408200-62408800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:62408200-62409200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr1:62408200-62409400	Strong transcription	Sigmoid Colon	Sigmoid Colon

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