Variant report

Variant	rs2251182
Chromosome Location	chr1:62393394-62393395
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10889271	0.82[CHB][hapmap];0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs10889272	0.82[CHB][hapmap];0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs10889277	0.82[CHB][hapmap]
rs10889278	0.83[ASN][1000 genomes]
rs10889279	0.83[ASN][1000 genomes]
rs11207869	0.86[ASN][1000 genomes]
rs11207877	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[ASN][1000 genomes]
rs1815464	0.81[EUR][1000 genomes]
rs2151124	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[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];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2365735	0.86[ASN][1000 genomes]
rs2482860	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2482861	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2482862	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2482863	1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2482865	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2482868	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2482881	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]
rs2482886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2482888	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2482889	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2498954	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs2498955	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2498958	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2498962	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[ASN][1000 genomes]
rs2498968	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]
rs3737108	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs6587949	0.82[CHB][hapmap]
rs6668270	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs6698695	0.82[CHB][hapmap]
rs7512525	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs7530734	0.90[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]

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	esv3693319	chr1:62207254-62402549	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2251182	HOOK1	cis	parietal	SCAN
rs2251182	EFCAB7	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62336000-62408600	Weak transcription	Pancreas	Pancrea
2	chr1:62340400-62399200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:62346200-62417600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:62350200-62397600	Weak transcription	Esophagus	oesophagus
5	chr1:62350600-62428200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:62350800-62395800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:62350800-62397800	Weak transcription	Primary T cells from cord blood	blood
8	chr1:62350800-62417600	Weak transcription	Ovary	ovary
9	chr1:62353600-62396000	Weak transcription	Fetal Kidney	kidney
10	chr1:62353800-62408800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:62361600-62408800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:62362000-62408600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:62372400-62408800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:62372400-62417600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:62374600-62410600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:62375200-62404600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:62376200-62417600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:62377200-62396600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:62379400-62393600	Weak transcription	Right Ventricle	heart
20	chr1:62380600-62408600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr1:62380800-62395800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:62380800-62410000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:62381000-62393600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:62381000-62408200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:62381000-62416000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:62381200-62394600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:62381200-62417400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:62381200-62418400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:62381600-62402800	Weak transcription	HepG2	liver
30	chr1:62382400-62393400	Weak transcription	Liver	Liver
31	chr1:62383400-62408000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:62384600-62403000	Weak transcription	Fetal Stomach	stomach
33	chr1:62384600-62408200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:62384600-62408800	Weak transcription	Fetal Intestine Large	intestine
35	chr1:62385000-62494200	Weak transcription	Aorta	Aorta
36	chr1:62385400-62394800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:62385400-62408400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:62385400-62408600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:62386000-62394800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:62386000-62408600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:62386200-62397000	Weak transcription	Fetal Intestine Small	intestine
42	chr1:62387000-62394800	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:62388400-62394600	Weak transcription	HMEC	breast
44	chr1:62388600-62394600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr1:62388800-62397400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:62389800-62396000	Weak transcription	NHEK	skin
47	chr1:62390000-62393600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:62391800-62393400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:62391800-62409000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:62392000-62408800	Weak transcription	Gastric	stomach

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