Variant report

Variant	rs2230600
Chromosome Location	chr4:87690998-87690999
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10016074	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10019950	0.82[ASN][1000 genomes]
rs10050311	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs1021101	0.83[TSI][hapmap]
rs1035191	0.81[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.85[ASN][1000 genomes]
rs10516778	0.88[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11097115	0.83[TSI][hapmap]
rs11561681	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12331502	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12503659	0.82[ASN][1000 genomes]
rs12510802	0.85[ASN][1000 genomes]
rs13113689	0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs1420621	0.84[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17012072	0.86[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17419627	0.83[TSI][hapmap]
rs17419929	0.83[TSI][hapmap]
rs17420607	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17420966	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17454154	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17454662	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17694112	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2006842	0.82[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.85[ASN][1000 genomes]
rs2054592	1.00[CEU][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2054593	0.85[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs2287147	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3775236	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs3775238	0.94[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3775239	0.85[JPT][hapmap];0.85[MEX][hapmap]
rs4263359	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4693150	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4693780	0.94[CEU][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4693784	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55670248	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57954319	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs67867077	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72665791	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72665795	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs969734	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830001	chr4:87585278-87748643	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2230600	LIN54	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87631200-87712200	Weak transcription	Aorta	Aorta
2	chr4:87635200-87737400	Weak transcription	Fetal Brain Male	brain
3	chr4:87639400-87739200	Weak transcription	A549	lung
4	chr4:87642200-87692600	Weak transcription	NH-A	brain
5	chr4:87642400-87735800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:87642600-87692400	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:87642600-87697600	Weak transcription	Brain Angular Gyrus	brain
8	chr4:87642600-87719200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr4:87655600-87704400	Weak transcription	Hela-S3	cervix
10	chr4:87661600-87710200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:87661600-87711400	Weak transcription	Brain Germinal Matrix	brain
12	chr4:87661600-87712000	Weak transcription	Esophagus	oesophagus
13	chr4:87661600-87737800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:87661800-87708000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:87661800-87712000	Weak transcription	Fetal Intestine Small	intestine
16	chr4:87661800-87728800	Weak transcription	Pancreas	Pancrea
17	chr4:87663000-87711400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:87665000-87692400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:87671800-87713000	Weak transcription	HSMMtube	muscle
20	chr4:87672000-87712200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr4:87672800-87710000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr4:87672800-87712000	Weak transcription	Lung	lung
23	chr4:87676200-87699600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:87677000-87711400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:87677200-87708600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr4:87678800-87699800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:87679000-87712000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:87679000-87712400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:87679200-87692200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr4:87679200-87699800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:87679400-87695400	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr4:87679400-87700200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:87679400-87702200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:87681000-87692400	Weak transcription	Brain Substantia Nigra	brain
35	chr4:87681000-87710200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:87682200-87701800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:87684200-87698000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:87684400-87691000	Weak transcription	Adipose Nuclei	Adipose
39	chr4:87684400-87691000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr4:87684400-87692200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr4:87684400-87692800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:87684400-87710000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr4:87684600-87692400	Weak transcription	Fetal Brain Female	brain
44	chr4:87684600-87692400	Weak transcription	Fetal Kidney	kidney
45	chr4:87685000-87691000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr4:87685000-87699400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:87685600-87697800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr4:87685600-87698800	Strong transcription	HMEC	breast
49	chr4:87685800-87699600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr4:87685800-87699800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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