Variant report

Variant	rs12500587
Chromosome Location	chr4:15580754-15580755
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15580223..15582658-chr4:15681473..15683314,2	K562	blood:

Variant related genes	Relation type
ENSG00000118564	Chromatin interaction
ENSG00000237765	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10008376	1.00[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs10008975	1.00[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs10214	1.00[CEU][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs1125378	0.84[CHD][hapmap]
rs11728084	0.86[EUR][1000 genomes]
rs12499412	0.91[EUR][1000 genomes]
rs12500770	0.91[EUR][1000 genomes]
rs12512883	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12644655	0.82[EUR][1000 genomes]
rs12651550	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13110674	0.97[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13120905	0.91[EUR][1000 genomes]
rs13129739	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13147590	0.90[EUR][1000 genomes]
rs1558572	0.84[CHD][hapmap]
rs1789	0.86[EUR][1000 genomes]
rs35414597	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4235379	0.90[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4270584	1.00[CEU][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4358397	0.88[ASN][1000 genomes]
rs4453929	0.83[EUR][1000 genomes]
rs4470622	0.84[EUR][1000 genomes]
rs4524378	0.96[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4557256	0.85[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs4616746	0.84[EUR][1000 genomes]
rs4631041	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4698402	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4698404	0.89[EUR][1000 genomes]
rs4698406	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4698407	0.89[EUR][1000 genomes]
rs4698409	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs61021642	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6414765	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6414767	0.89[EUR][1000 genomes]
rs6449153	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6449161	0.82[CEU][hapmap]
rs6812708	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs6850169	0.81[EUR][1000 genomes]
rs6850422	1.00[CEU][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes]
rs7438356	1.00[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs7662032	0.89[EUR][1000 genomes]
rs7685083	1.00[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs7687003	0.85[EUR][1000 genomes]
rs7688984	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7690362	0.89[ASN][1000 genomes]
rs7696127	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7696938	0.80[ASW][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.84[YRI][hapmap];0.89[ASN][1000 genomes]
rs8180240	0.91[ASN][1000 genomes]
rs9918079	0.85[YRI][hapmap]
rs9997068	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12500587	FAM200B	cis	parietal	SCAN
rs12500587	FBXL5	Cis_1M	lymphoblastoid	RTeQTL
rs12500587	CC2D2A	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15517800-15593600	Weak transcription	HUVEC	blood vessel
2	chr4:15537400-15621000	Weak transcription	Hela-S3	cervix
3	chr4:15546000-15589600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:15550000-15617800	Weak transcription	Thymus	Thymus
5	chr4:15554600-15601400	Weak transcription	A549	lung
6	chr4:15555800-15589400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:15556000-15603200	Weak transcription	Fetal Thymus	thymus
8	chr4:15560200-15580800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:15564000-15600600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:15564400-15603200	Weak transcription	HMEC	breast
11	chr4:15564600-15603600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:15565400-15612600	Weak transcription	Brain Substantia Nigra	brain
13	chr4:15565400-15621400	Weak transcription	Esophagus	oesophagus
14	chr4:15565600-15604200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:15565600-15611400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:15565800-15605000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr4:15566200-15596800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr4:15568400-15655600	Weak transcription	Gastric	stomach
19	chr4:15568600-15589400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:15569600-15588600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:15569600-15596400	Weak transcription	NHDF-Ad	bronchial
22	chr4:15569600-15603600	Weak transcription	Spleen	Spleen
23	chr4:15569600-15604200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:15570200-15601800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:15570600-15588200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:15570600-15602000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:15570600-15602000	Weak transcription	Pancreas	Pancrea
28	chr4:15570800-15582000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:15570800-15588800	Weak transcription	Psoas Muscle	Psoas
30	chr4:15570800-15589600	Weak transcription	Lung	lung
31	chr4:15571000-15597200	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:15571200-15588000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:15571200-15588800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr4:15571400-15596000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr4:15571800-15585800	Weak transcription	Brain Anterior Caudate	brain
36	chr4:15572000-15593400	Weak transcription	Fetal Brain Male	brain
37	chr4:15572200-15583200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:15572200-15585800	Weak transcription	Primary B cells from cord blood	blood
39	chr4:15572200-15586800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr4:15572200-15588200	Weak transcription	Adipose Nuclei	Adipose
41	chr4:15572200-15588600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr4:15572200-15591600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:15572200-15593600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:15572200-15595600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:15572200-15601200	Weak transcription	NHLF	lung
46	chr4:15572200-15601800	Weak transcription	Brain Angular Gyrus	brain
47	chr4:15572200-15601800	Weak transcription	NHEK	skin
48	chr4:15572200-15604000	Weak transcription	Primary T cells from cord blood	blood
49	chr4:15572200-15604200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr4:15572400-15596200	Weak transcription	Ovary	ovary

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