Variant report

Variant	rs7519752
Chromosome Location	chr1:227400418-227400419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227361494..227363417-chr1:227400194..227402831,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1007574	0.81[EUR][1000 genomes]
rs10429872	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495255	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs10495260	0.91[CEU][hapmap];0.84[GIH][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs10799379	0.92[LWK][hapmap];0.85[YRI][hapmap]
rs10799384	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs10799391	0.81[EUR][1000 genomes]
rs10799396	0.81[EUR][1000 genomes]
rs10799397	0.82[EUR][1000 genomes]
rs10799409	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799410	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916092	0.81[EUR][1000 genomes]
rs10916097	0.81[EUR][1000 genomes]
rs10916106	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916108	0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916111	0.80[EUR][1000 genomes]
rs10916118	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12035986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12044287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12065126	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12125514	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap]
rs12135061	0.80[EUR][1000 genomes]
rs12137591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12140758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap]
rs12141869	0.80[EUR][1000 genomes]
rs12565056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12565871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12566059	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12569227	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12742066	0.87[EUR][1000 genomes]
rs1304324	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs1913344	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1929869	0.94[JPT][hapmap];1.00[YRI][hapmap]
rs2102638	0.91[ASN][1000 genomes]
rs2953638	0.85[CEU][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap]
rs2953652	0.94[JPT][hapmap]
rs2953655	0.94[JPT][hapmap]
rs3014252	0.94[JPT][hapmap]
rs3014253	0.94[JPT][hapmap]
rs3014256	0.85[CEU][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs3014267	0.83[JPT][hapmap]
rs34084723	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34875093	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35738984	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3795457	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4339829	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[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];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4653797	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4653812	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6685106	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6685954	0.81[EUR][1000 genomes]
rs6692294	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6697272	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750172	0.81[EUR][1000 genomes]
rs7516326	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7537038	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs955704	0.91[CEU][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9887962	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats 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	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7519752	CABC1	cis	cerebellum	SCAN
rs7519752	DNAH14	cis	parietal	SCAN
rs7519752	PARP1	cis	cerebellum	SCAN
rs7519752	PRSS38	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227333400-227405600	Weak transcription	Adipose Nuclei	Adipose
2	chr1:227346800-227403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:227346800-227405800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:227346800-227406800	Weak transcription	Fetal Kidney	kidney
5	chr1:227348200-227401600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:227348200-227408400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:227348200-227412200	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:227360800-227401200	Weak transcription	Hela-S3	cervix
9	chr1:227370000-227413600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:227374400-227401600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:227374600-227401600	Weak transcription	Left Ventricle	heart
12	chr1:227375600-227410800	Weak transcription	HepG2	liver
13	chr1:227376600-227412600	Weak transcription	Fetal Lung	lung
14	chr1:227378400-227401000	Weak transcription	Placenta	Placenta
15	chr1:227380200-227402200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:227380200-227405200	Weak transcription	Gastric	stomach
17	chr1:227380200-227421800	Weak transcription	Ovary	ovary
18	chr1:227380400-227404000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:227380400-227406800	Weak transcription	NHDF-Ad	bronchial
20	chr1:227381600-227406600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:227382000-227414000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:227383600-227421800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:227386200-227433400	Weak transcription	Fetal Stomach	stomach
24	chr1:227386400-227413800	Weak transcription	Brain Anterior Caudate	brain
25	chr1:227386800-227406600	Weak transcription	Fetal Intestine Small	intestine
26	chr1:227387000-227413600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:227387400-227414000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:227390600-227413600	Weak transcription	Small Intestine	intestine
29	chr1:227396800-227413600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:227397000-227406800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:227398200-227413600	Weak transcription	NHLF	lung
32	chr1:227398400-227400800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:227398600-227401600	Weak transcription	Pancreas	Pancrea
34	chr1:227398600-227407000	Weak transcription	Lung	lung
35	chr1:227398800-227401400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:227398800-227405600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:227398800-227407000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:227398800-227411200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:227398800-227413800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:227399000-227402200	Weak transcription	Psoas Muscle	Psoas
41	chr1:227399000-227406400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:227399000-227406400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:227399000-227408800	Weak transcription	Liver	Liver
44	chr1:227399200-227406800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:227399200-227407000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:227399400-227402800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:227399400-227411200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:227399400-227415400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:227399600-227401400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:227399600-227413200	Weak transcription	HSMM	muscle

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