Variant report

Variant	rs608358
Chromosome Location	chr1:120289407-120289408
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120286920..120290208-chr1:120298529..120301740,3	K562	blood:
2	chr1:120261924..120264165-chr1:120287525..120289595,2	K562	blood:
3	chr1:120281402..120284311-chr1:120289109..120290703,2	MCF-7	breast:
4	chr1:120288807..120290729-chr1:120293224..120295388,2	MCF-7	breast:
5	chr1:120282346..120286075-chr1:120287322..120291391,4	K562	blood:

Variant related genes	Relation type
ENSG00000092621	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12562383	0.82[CHB][hapmap]
rs1441008	0.86[CHB][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs518027	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs522277	0.86[CEU][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs543703	0.86[CEU][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs566864	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs590825	0.86[CEU][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs591162	0.86[CEU][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs593911	0.86[CEU][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs610404	0.86[CEU][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs627070	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs649733	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs651347	0.86[CEU][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs667246	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs689198	0.85[CEU][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831204	chr1:120266449-120314091	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs608358	CD58	cis	cerebellum	SCAN
rs608358	VANGL1	cis	parietal	SCAN
rs608358	ATP1A1	cis	parietal	SCAN
rs608358	SPAG17	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120263400-120291400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:120279200-120290600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr1:120282000-120293400	Weak transcription	Aorta	Aorta
4	chr1:120285600-120292200	Weak transcription	Lung	lung
5	chr1:120285800-120289600	Weak transcription	Ovary	ovary
6	chr1:120286000-120289600	Weak transcription	Pancreas	Pancrea
7	chr1:120286000-120290000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:120286000-120290200	Weak transcription	NHLF	lung
9	chr1:120286600-120289600	Enhancers	Liver	Liver
10	chr1:120286600-120289600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:120286600-120291400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr1:120286800-120289600	Weak transcription	Esophagus	oesophagus
13	chr1:120286800-120289800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:120286800-120289800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:120286800-120290800	Weak transcription	Adipose Nuclei	Adipose
16	chr1:120286800-120290800	Weak transcription	Colonic Mucosa	Colon
17	chr1:120286800-120290800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:120286800-120290800	Weak transcription	Fetal Lung	lung
19	chr1:120286800-120297800	Weak transcription	Right Ventricle	heart
20	chr1:120286800-120302200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:120286800-120310000	Weak transcription	Psoas Muscle	Psoas
22	chr1:120287000-120290800	Weak transcription	Spleen	Spleen
23	chr1:120287000-120301800	Weak transcription	Left Ventricle	heart
24	chr1:120287000-120308200	Weak transcription	Stomach Mucosa	stomach
25	chr1:120287200-120289600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:120287200-120290000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:120287200-120290000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:120287200-120290000	Weak transcription	Hela-S3	cervix
29	chr1:120287200-120290400	Weak transcription	Fetal Heart	heart
30	chr1:120287200-120293400	Weak transcription	Right Atrium	heart
31	chr1:120287200-120308800	Weak transcription	Fetal Kidney	kidney
32	chr1:120287400-120289600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:120287400-120291200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:120287600-120289800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:120287600-120289800	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:120287600-120290400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:120287800-120290400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:120287800-120291400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr1:120288000-120290600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:120288000-120306800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr1:120288200-120289600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:120288200-120290600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:120288400-120291600	Weak transcription	Fetal Intestine Large	intestine
44	chr1:120288600-120290200	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr1:120288600-120290200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:120288600-120290800	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr1:120288800-120289800	Enhancers	H9 Cell Line	embryonic stem cell
48	chr1:120288800-120290200	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr1:120288800-120290800	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr1:120288800-120291000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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