Variant report

Variant	rs1010476
Chromosome Location	chr1:93596936-93596937
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93543048..93545567-chr1:93596297..93598631,2	K562	blood:
2	chr1:93579998..93581880-chr1:93596682..93599849,3	K562	blood:
3	chr1:93543048..93546270-chr1:93596297..93598631,3	K562	blood:
4	chr1:93596596..93599097-chr1:93600778..93604070,3	K562	blood:

Variant related genes	Relation type
ENSG00000143033	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1060622	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs11164870	0.82[CHB][hapmap]
rs11164876	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs11164879	0.81[CHB][hapmap]
rs12030549	0.82[CHB][hapmap]
rs12030843	0.95[CHB][hapmap]
rs12033147	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12038046	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12038699	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs12044557	0.95[CHB][hapmap];0.88[CHD][hapmap]
rs12118262	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs12128131	0.89[CHB][hapmap]
rs12563120	0.95[CHB][hapmap];0.88[CHD][hapmap]
rs1335679	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs1474927	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs1572343	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs1856027	0.88[CHD][hapmap]
rs2031225	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs2255722	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2281524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2281525	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs2295423	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs2296558	0.81[CHB][hapmap]
rs2391254	0.82[CHB][hapmap]
rs2484486	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2749732	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2765545	0.89[CHD][hapmap]
rs2783489	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs2783490	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2783493	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2783495	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2783496	0.89[ASN][1000 genomes]
rs2783497	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2783499	0.95[CHB][hapmap];0.88[CHD][hapmap]
rs2783500	1.00[CHB][hapmap]
rs2783501	0.95[CHB][hapmap]
rs2783505	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2815406	0.94[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815429	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[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];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3754186	0.82[CHB][hapmap]
rs3904665	0.82[CHB][hapmap]
rs3904666	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs4000699	0.82[CHB][hapmap]
rs4240966	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs4484937	0.95[CHB][hapmap];0.87[CHD][hapmap]
rs4847235	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs4847399	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs4847408	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs489183	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531358	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs556446	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs579138	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs612037	0.82[CHB][hapmap]
rs61799470	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs622608	0.81[CHB][hapmap]
rs6541349	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs6541401	0.82[CHB][hapmap]
rs6541404	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs6682670	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs6703310	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs693737	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs7513705	0.86[CHB][hapmap]
rs7517363	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs7535628	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs7539307	0.86[CHB][hapmap]
rs797668	0.82[CHB][hapmap]
rs797680	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1010476	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs1010476	DR1	cis	parietal	SCAN
rs1010476	CCDC18	cis	parietal	SCAN
rs1010476	GLMN	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93546200-93602200	Weak transcription	Aorta	Aorta
2	chr1:93547600-93600000	Weak transcription	HSMMtube	muscle
3	chr1:93548000-93601800	Weak transcription	NHLF	lung
4	chr1:93565200-93625200	Weak transcription	Stomach Mucosa	stomach
5	chr1:93571400-93602200	Weak transcription	Colonic Mucosa	Colon
6	chr1:93572400-93599600	Weak transcription	Spleen	Spleen
7	chr1:93573400-93627000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:93573800-93609000	Strong transcription	Fetal Thymus	thymus
9	chr1:93574200-93609000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:93574600-93609000	Strong transcription	Dnd41	blood
11	chr1:93574600-93630200	Weak transcription	Right Ventricle	heart
12	chr1:93577200-93597000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:93577800-93601600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:93578800-93613600	Weak transcription	Psoas Muscle	Psoas
15	chr1:93578800-93620600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:93580000-93624000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:93580200-93643600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:93581000-93599200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:93581200-93616800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:93582400-93599800	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:93582400-93600000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:93582400-93620400	Weak transcription	Small Intestine	intestine
23	chr1:93582400-93642800	Weak transcription	Gastric	stomach
24	chr1:93582600-93600000	Weak transcription	Ovary	ovary
25	chr1:93583000-93601400	Weak transcription	Brain Substantia Nigra	brain
26	chr1:93583000-93604200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:93583200-93602000	Weak transcription	NHDF-Ad	bronchial
28	chr1:93583200-93628800	Weak transcription	Brain Angular Gyrus	brain
29	chr1:93583600-93599600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:93583600-93599600	Weak transcription	Left Ventricle	heart
31	chr1:93583600-93600000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:93583600-93600800	Weak transcription	Fetal Brain Female	brain
33	chr1:93583600-93613800	Weak transcription	Lung	lung
34	chr1:93583600-93623800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:93583600-93635400	Weak transcription	Pancreas	Pancrea
36	chr1:93584200-93600000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr1:93584200-93600000	Weak transcription	Osteobl	bone
38	chr1:93584600-93600000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:93584600-93601000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:93585200-93609200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:93585400-93600000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:93585800-93601800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr1:93585800-93642200	Weak transcription	Esophagus	oesophagus
44	chr1:93586200-93597000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:93586200-93623400	Weak transcription	Fetal Brain Male	brain
46	chr1:93586400-93599600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr1:93586400-93600000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:93586400-93600200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr1:93586400-93600200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:93586600-93599600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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