Variant report

Variant	rs1041602
Chromosome Location	chr1:57013198-57013199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:57010110..57012912-chr1:57012991..57015582,3	K562	blood:
2	chr1:56879071..56881393-chr1:57012457..57015249,2	MCF-7	breast:
3	chr1:57010225..57012912-chr1:57013019..57015582,2	K562	blood:

Variant related genes	Relation type
ENSG00000223956	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1418977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17416285	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs17470169	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1759753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1777279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1819750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3927760	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3927761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41487448	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772578	0.96[AMR][1000 genomes]
rs61772592	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772595	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772618	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772626	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674131	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688009	0.89[CEU][hapmap]
rs857131	1.00[CHB][hapmap]
rs9437006	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1041602	RAB31	trans	lymphoblastoid	seeQTL
rs1041602	PCSK9	cis	cerebellum	SCAN
rs1041602	DIO1	cis	cerebellum	SCAN
rs1041602	LRP8	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56987000-57015000	Genic enhancers	NHDF-Ad	bronchial
2	chr1:57001200-57018800	Weak transcription	A549	lung
3	chr1:57001800-57018600	Weak transcription	Small Intestine	intestine
4	chr1:57001800-57021800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:57002800-57013200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:57002800-57018600	Weak transcription	Thymus	Thymus
7	chr1:57003200-57019800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:57003400-57015400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:57003600-57013200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:57004000-57014800	Weak transcription	Fetal Thymus	thymus
11	chr1:57004400-57013200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:57005600-57013800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:57005800-57013200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:57007400-57028400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:57007600-57013400	Weak transcription	Osteobl	bone
16	chr1:57007800-57015400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:57008600-57013200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:57008600-57014800	Weak transcription	Brain Germinal Matrix	brain
19	chr1:57008600-57015000	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr1:57008800-57013400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:57009200-57014600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr1:57009600-57028000	Weak transcription	Fetal Kidney	kidney
23	chr1:57009800-57013200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:57010400-57019200	Enhancers	H1 Cell Line	embryonic stem cell
25	chr1:57010400-57019600	Enhancers	Right Ventricle	heart
26	chr1:57010600-57017200	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr1:57011000-57013400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:57011000-57013600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:57011000-57017200	Enhancers	Brain Anterior Caudate	brain
30	chr1:57011000-57020200	Enhancers	Brain Hippocampus Middle	brain
31	chr1:57011600-57015000	Weak transcription	Aorta	Aorta
32	chr1:57011600-57016600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:57011800-57013200	Weak transcription	Lung	lung
34	chr1:57011800-57014600	Enhancers	Colon Smooth Muscle	Colon
35	chr1:57011800-57015600	Weak transcription	Fetal Stomach	stomach
36	chr1:57011800-57018000	Enhancers	Brain Substantia Nigra	brain
37	chr1:57012000-57013200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:57012000-57013200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:57012000-57013200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:57012000-57013200	Weak transcription	Esophagus	oesophagus
41	chr1:57012000-57013200	Weak transcription	Gastric	stomach
42	chr1:57012000-57013200	Weak transcription	Ovary	ovary
43	chr1:57012000-57013200	Weak transcription	Pancreas	Pancrea
44	chr1:57012000-57013200	Weak transcription	Right Atrium	heart
45	chr1:57012000-57013800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:57012000-57014200	Strong transcription	NHLF	lung
47	chr1:57012000-57014400	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr1:57012000-57016800	Enhancers	HepG2	liver
49	chr1:57012000-57017000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:57012000-57017000	Weak transcription	Spleen	Spleen

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