Variant report

Variant	rs10889271
Chromosome Location	chr1:62400487-62400488
allele	C/T
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:29)

rs_ID	r²[population]
rs10889272	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10889277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10889278	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10889279	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11207864	0.91[CHB][hapmap]
rs11207869	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11207877	0.82[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11207878	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12135923	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2151124	0.82[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs2251182	0.82[CHB][hapmap];0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs2365735	0.86[ASN][1000 genomes]
rs2482868	0.83[ASN][1000 genomes]
rs2482881	0.82[CHB][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs2482886	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs2482889	0.82[ASN][1000 genomes]
rs2498954	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2498955	0.83[ASN][1000 genomes]
rs2498958	0.83[ASN][1000 genomes]
rs2498962	0.82[CHB][hapmap];0.90[CHD][hapmap];0.83[ASN][1000 genomes]
rs2498968	0.83[CHD][hapmap]
rs35506226	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3737108	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61775620	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6587949	1.00[CHB][hapmap]
rs6668270	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.93[ASN][1000 genomes]
rs6698695	1.00[CHB][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7512525	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7530734	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]

Variant overlapped rSNPs/rCNVs (count:7 , 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
5	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
6	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
7	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10889271	DAB1	cis	parietal	SCAN
rs10889271	HOOK1	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	chr1:62346200-62417600	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	chr1:62375200-62404600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:62376200-62417600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:62380600-62408600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr1:62380800-62410000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:62381000-62408200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:62381000-62416000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:62381200-62417400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:62381200-62418400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:62381600-62402800	Weak transcription	HepG2	liver
20	chr1:62383400-62408000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:62384600-62403000	Weak transcription	Fetal Stomach	stomach
22	chr1:62384600-62408200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:62384600-62408800	Weak transcription	Fetal Intestine Large	intestine
24	chr1:62385000-62494200	Weak transcription	Aorta	Aorta
25	chr1:62385400-62408400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:62385400-62408600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:62386000-62408600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:62391800-62409000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:62392000-62408800	Weak transcription	Gastric	stomach
30	chr1:62392600-62408600	Weak transcription	Stomach Mucosa	stomach
31	chr1:62392600-62408800	Weak transcription	Left Ventricle	heart
32	chr1:62393800-62402800	Weak transcription	Hela-S3	cervix
33	chr1:62393800-62422400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr1:62395000-62408600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr1:62395000-62410800	Weak transcription	Liver	Liver
36	chr1:62395800-62408200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr1:62396200-62408600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:62396200-62416000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:62396200-62417200	Weak transcription	HMEC	breast
40	chr1:62396400-62408200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:62396400-62408600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:62396400-62418000	Weak transcription	Fetal Kidney	kidney
43	chr1:62397400-62408200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:62397600-62408600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:62398000-62408200	Weak transcription	NHEK	skin
46	chr1:62398200-62402400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:62398200-62408400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr1:62398200-62408600	Weak transcription	Esophagus	oesophagus
49	chr1:62398600-62405400	Weak transcription	Fetal Intestine Small	intestine
50	chr1:62398800-62408600	Weak transcription	Rectal Mucosa Donor 31	rectum

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