Variant report

Variant	rs1230210
Chromosome Location	chr4:99967691-99967692
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:99916905..99919030-chr4:99967654..99969296,2	K562	blood:
2	chr4:99961580..99964150-chr4:99966908..99969886,2	MCF-7	breast:
3	chr4:99916503..99920341-chr4:99967217..99969566,4	K562	blood:

Variant related genes	Relation type
ENSG00000164024	Chromatin interaction
ENSG00000265213	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1020624	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037476	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230161	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230162	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230165	1.00[LWK][hapmap]
rs1230171	0.83[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230176	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230177	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230181	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230184	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230185	0.91[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230187	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230191	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230198	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230202	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2004995	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602831	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3018051	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3018052	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1230210	CENPE	cis	cerebellum	SCAN
rs1230210	ADH5	cis	cerebellum	SCAN
rs1230210	METAP1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99931600-99971400	Weak transcription	Aorta	Aorta
2	chr4:99932600-99969800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr4:99942200-99969600	Weak transcription	Fetal Brain Female	brain
4	chr4:99944200-99968800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:99944200-99969600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:99944200-99979000	Weak transcription	Colonic Mucosa	Colon
7	chr4:99944200-99979200	Weak transcription	Right Ventricle	heart
8	chr4:99944400-99971600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:99944400-99979200	Weak transcription	Brain Hippocampus Middle	brain
10	chr4:99945000-99969600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:99946000-99976800	Weak transcription	Stomach Mucosa	stomach
12	chr4:99946200-99970000	Weak transcription	Brain Anterior Caudate	brain
13	chr4:99946200-99977000	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:99946400-99969000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:99946400-99969400	Weak transcription	Placenta	Placenta
16	chr4:99946400-99973600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:99946400-99979000	Weak transcription	Esophagus	oesophagus
18	chr4:99946600-99970000	Weak transcription	Hela-S3	cervix
19	chr4:99947000-99969600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:99947000-99969800	Weak transcription	Ovary	ovary
21	chr4:99947000-99979000	Weak transcription	Gastric	stomach
22	chr4:99947000-99979200	Weak transcription	Pancreas	Pancrea
23	chr4:99947400-99982600	Weak transcription	Psoas Muscle	Psoas
24	chr4:99949000-99979000	Weak transcription	Small Intestine	intestine
25	chr4:99949200-99968400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:99949600-99969400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:99949600-99973200	Weak transcription	Fetal Kidney	kidney
28	chr4:99953800-99969800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr4:99954000-99971600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:99954000-99999200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr4:99954600-99976600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:99954800-99977000	Weak transcription	Brain Substantia Nigra	brain
33	chr4:99955000-99969800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:99955400-99968600	Weak transcription	Fetal Heart	heart
35	chr4:99955400-99980800	Weak transcription	HSMMtube	muscle
36	chr4:99955600-99969200	Weak transcription	NH-A	brain
37	chr4:99956200-99995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:99956400-99970000	Weak transcription	NHLF	lung
39	chr4:99958000-99970200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr4:99959400-99976200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr4:99959600-99976000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr4:99959800-99973600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:99959800-100000200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr4:99960000-99970000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr4:99960200-99969400	Weak transcription	Liver	Liver
46	chr4:99960400-99969600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:99960400-99969800	Weak transcription	A549	lung
48	chr4:99960400-99973400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:99961600-99976200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:99962400-99969600	Weak transcription	Spleen	Spleen

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