Variant report

Variant	rs7555139
Chromosome Location	chr1:225716241-225716242
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225712005..225714955-chr1:225715137..225718400,3	K562	blood:
2	chr1:225713990..225716472-chr1:225723399..225725793,2	K562	blood:
3	chr1:225710717..225715059-chr1:225715137..225718400,6	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10753406	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10799311	0.88[EUR][1000 genomes]
rs10799313	0.82[ASN][1000 genomes]
rs10799314	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10799316	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs10799317	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10799318	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10799319	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10915828	0.93[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap]
rs10915830	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10915833	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10915834	0.93[EUR][1000 genomes]
rs10915835	0.82[ASN][1000 genomes]
rs10915837	0.84[ASN][1000 genomes]
rs10915839	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10915847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11584675	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12028305	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222440	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.82[ASN][1000 genomes]
rs12729655	0.84[ASN][1000 genomes]
rs2639703	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2639712	0.81[TSI][hapmap]
rs2639716	0.83[EUR][1000 genomes]
rs2657564	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2657569	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs2840958	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2840967	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs2840968	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs3820226	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3856156	0.95[EUR][1000 genomes]
rs4653643	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs476540	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs487591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs498350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs510293	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs511649	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs516249	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs551996	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs554744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs554992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs561656	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs576861	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6426076	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6426078	0.82[ASN][1000 genomes]
rs6668770	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6676201	0.84[ASN][1000 genomes]
rs6678806	0.83[ASN][1000 genomes]
rs6697783	0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs6702555	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6751	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs712062	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7515907	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7515963	0.84[ASN][1000 genomes]
rs7524766	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7540181	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7541598	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7555553	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs812523	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs947034	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9804142	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv4720	chr1:225673218-225718009	Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7555139	C1orf58	cis	parietal	SCAN
rs7555139	DHX33	trans	multi-tissue	Pritchard
rs7555139	LBR	cis	Artery Tibial	GTEx
rs7555139	C1orf109	trans	brain	seeQTL
rs7555139	ENAH	cis	normal skin	skin_eQTL
rs7555139	MIXL1	cis	cerebellum	SCAN
rs7555139	PYCR2	cis	cerebellum	SCAN
rs7555139	RP11-496N12.9	cis	Thyroid	GTEx
rs7555139	DUSP10	cis	parietal	SCAN
rs7555139	USP10	trans	brain	seeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225689200-225721000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:225695600-225721200	Weak transcription	Fetal Kidney	kidney
3	chr1:225697200-225716600	Weak transcription	Right Atrium	heart
4	chr1:225697400-225722600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:225698600-225721000	Weak transcription	Small Intestine	intestine
6	chr1:225700000-225726400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:225700000-225726400	Weak transcription	HMEC	breast
8	chr1:225701400-225727200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:225701400-225744400	Weak transcription	HUVEC	blood vessel
10	chr1:225701400-225747000	Weak transcription	Hela-S3	cervix
11	chr1:225704200-225721000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:225705600-225717600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:225705600-225747400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:225705800-225716800	Weak transcription	HepG2	liver
15	chr1:225705800-225717000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:225705800-225717400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:225705800-225717400	Weak transcription	Esophagus	oesophagus
18	chr1:225705800-225718800	Weak transcription	Lung	lung
19	chr1:225705800-225726600	Weak transcription	NHEK	skin
20	chr1:225707000-225717400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:225707200-225716600	Weak transcription	Fetal Stomach	stomach
22	chr1:225707200-225717600	Weak transcription	Aorta	Aorta
23	chr1:225707200-225726600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:225707200-225755000	Weak transcription	Gastric	stomach
25	chr1:225707400-225716600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:225707400-225716600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:225707400-225717000	Weak transcription	NHLF	lung
28	chr1:225707400-225726600	Weak transcription	Brain Angular Gyrus	brain
29	chr1:225707600-225716600	Weak transcription	NHDF-Ad	bronchial
30	chr1:225707600-225716800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:225709000-225721000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr1:225709200-225720000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:225711000-225718800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:225711200-225718800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:225711400-225726600	Weak transcription	Fetal Brain Female	brain
36	chr1:225711600-225720600	Weak transcription	Fetal Intestine Small	intestine
37	chr1:225711600-225720600	Weak transcription	HSMMtube	muscle
38	chr1:225711600-225721200	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:225712400-225717000	Weak transcription	Fetal Intestine Large	intestine
40	chr1:225712400-225719200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:225712400-225729600	Weak transcription	Right Ventricle	heart
42	chr1:225712800-225719000	Strong transcription	Osteobl	bone
43	chr1:225713000-225719000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:225713600-225716400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:225713600-225719400	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr1:225713800-225721000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:225714200-225719200	Strong transcription	A549	lung
48	chr1:225714400-225716600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:225714400-225717400	Enhancers	Brain Germinal Matrix	brain
50	chr1:225714800-225729600	Weak transcription	Ovary	ovary

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