Variant report

Variant	rs4512610
Chromosome Location	chr1:227252451-227252452
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	chr1:227248469..227250587-chr1:227251655..227253321,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1007574	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10495260	0.91[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10495267	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799379	0.84[LWK][hapmap]
rs10799383	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10799384	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10799391	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10799396	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10799397	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10916083	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10916084	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10916085	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10916086	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10916089	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10916090	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916092	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10916097	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12024326	0.86[CHB][hapmap]
rs12026688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12031609	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12035986	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs12036915	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12044287	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs12047828	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12073220	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12125514	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12129006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12135061	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12137591	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs12140758	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12141869	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12144369	0.85[AFR][1000 genomes]
rs12563165	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12565056	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12565871	1.00[CEU][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap]
rs12742066	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1304324	1.00[CEU][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1320490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1464079	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1888827	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs1913344	0.88[EUR][1000 genomes]
rs1929868	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1929869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2095016	0.83[ASN][1000 genomes]
rs34708504	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3818694	0.92[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs4653797	0.81[EUR][1000 genomes]
rs56260717	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6662443	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674641	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6682849	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6684284	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6684433	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6685954	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72750172	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7529970	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs955704	0.91[CEU][hapmap]
rs9887962	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv997751	chr1:227196502-227263537	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1011654	chr1:227196502-227308416	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1014423	chr1:227201253-227268843	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1012482	chr1:227212024-227271750	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv873239	chr1:227222125-227361072	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv468227	chr1:227223736-227340790	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv549269	chr1:227223736-227340790	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv998420	chr1:227228591-227275031	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv873240	chr1:227228946-227361072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv873241	chr1:227242247-227361072	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4512610	PRSS38	cis	parietal	SCAN
rs4512610	PARP1	cis	cerebellum	SCAN
rs4512610	CABC1	cis	cerebellum	SCAN
rs4512610	DNAH14	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227177400-227255200	Weak transcription	Small Intestine	intestine
3	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
4	chr1:227190600-227272600	Weak transcription	Lung	lung
5	chr1:227203000-227278800	Weak transcription	Pancreas	Pancrea
6	chr1:227209000-227272400	Weak transcription	Fetal Intestine Small	intestine
7	chr1:227209200-227301600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
9	chr1:227216800-227287600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:227217000-227264400	Weak transcription	NHLF	lung
11	chr1:227217000-227271400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:227217000-227278800	Weak transcription	Placenta	Placenta
13	chr1:227220600-227255800	Weak transcription	Gastric	stomach
14	chr1:227220600-227272600	Weak transcription	Aorta	Aorta
15	chr1:227220600-227288000	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:227220800-227256800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:227222000-227253000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:227222600-227256800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:227226600-227270800	Weak transcription	Fetal Brain Female	brain
20	chr1:227226800-227260400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:227226800-227272400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:227226800-227278400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:227226800-227285600	Weak transcription	Brain Germinal Matrix	brain
24	chr1:227227000-227256600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:227227000-227272200	Weak transcription	Fetal Heart	heart
26	chr1:227227000-227282200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:227227400-227253000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:227227400-227256400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:227227400-227256800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:227227400-227259800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:227227400-227272400	Weak transcription	Ovary	ovary
32	chr1:227227400-227281200	Weak transcription	Fetal Kidney	kidney
33	chr1:227227400-227284200	Weak transcription	Brain Angular Gyrus	brain
34	chr1:227227600-227259200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:227228000-227277000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:227232000-227256600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:227232800-227279200	Weak transcription	Stomach Mucosa	stomach
38	chr1:227234200-227253000	Weak transcription	Fetal Stomach	stomach
39	chr1:227234400-227252800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:227235400-227254400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:227235800-227253000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:227235800-227256600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:227235800-227256800	Weak transcription	A549	lung
44	chr1:227235800-227257000	Weak transcription	NHDF-Ad	bronchial
45	chr1:227235800-227271000	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:227236000-227286200	Weak transcription	Fetal Brain Male	brain
47	chr1:227238200-227256800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr1:227238400-227270600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:227238600-227278400	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:227239800-227271200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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