Variant report

Variant	rs13188662
Chromosome Location	chr5:52091647-52091648
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52087164..52092719-chr5:52094045..52097200,6	MCF-7	breast:
2	chr5:52083583..52086241-chr5:52089326..52091868,2	K562	blood:
3	chr5:52090515..52092112-chr5:52101180..52104170,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152684	Chromatin interaction
ENSG00000248898	Chromatin interaction
ENSG00000213949	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10512992	0.89[CHB][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.86[ASN][1000 genomes]
rs10940270	0.89[ASW][hapmap]
rs12652120	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12653042	0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13158244	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13182946	0.96[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13189629	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2454581	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2938796	0.96[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6879140	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6883810	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][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	esv2754787	chr5:51688543-52193243	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1027410	chr5:52022713-52103360	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1020640	chr5:52058830-52120858	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer 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	18 gene(s)	inside rSNPs	diseases
7	nsv830295	chr5:52084532-52257696	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13188662	BAT2L1	trans	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52084800-52093400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:52085200-52094400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:52085200-52094400	Weak transcription	A549	lung
4	chr5:52085200-52094400	Weak transcription	NHEK	skin
5	chr5:52085400-52093000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:52085400-52094400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:52085400-52094400	Weak transcription	HMEC	breast
8	chr5:52085800-52094800	Weak transcription	Brain Anterior Caudate	brain
9	chr5:52086000-52093400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:52086000-52094200	Weak transcription	Fetal Intestine Large	intestine
11	chr5:52086200-52093800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:52086200-52093800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:52086200-52094200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:52086400-52092600	Weak transcription	Fetal Intestine Small	intestine
15	chr5:52086400-52094400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:52086800-52093200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr5:52086800-52093200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr5:52086800-52094200	Weak transcription	Fetal Stomach	stomach
19	chr5:52087200-52093800	Weak transcription	Primary T cells from cord blood	blood
20	chr5:52087200-52094400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr5:52087400-52092000	Weak transcription	NHLF	lung
22	chr5:52087400-52092600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr5:52087400-52093400	Weak transcription	NHDF-Ad	bronchial
24	chr5:52087400-52094000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr5:52087400-52094200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:52087400-52094400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr5:52087400-52094400	Enhancers	HepG2	liver
28	chr5:52087400-52094600	Weak transcription	Right Atrium	heart
29	chr5:52087400-52095200	Weak transcription	Left Ventricle	heart
30	chr5:52087600-52092600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:52088400-52091800	Enhancers	Rectal Smooth Muscle	rectum
32	chr5:52088600-52094600	Enhancers	Adipose Nuclei	Adipose
33	chr5:52088800-52093600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr5:52089000-52092400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:52089000-52092800	Weak transcription	Small Intestine	intestine
36	chr5:52089000-52093400	Weak transcription	Psoas Muscle	Psoas
37	chr5:52089000-52094200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr5:52089400-52093600	Weak transcription	Hela-S3	cervix
39	chr5:52089600-52093400	Enhancers	Dnd41	blood
40	chr5:52089800-52093400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr5:52090400-52092000	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr5:52090600-52091800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr5:52090600-52094400	Enhancers	Colon Smooth Muscle	Colon
44	chr5:52090800-52094000	Weak transcription	Stomach Mucosa	stomach
45	chr5:52091200-52092000	Weak transcription	Fetal Kidney	kidney
46	chr5:52091200-52094800	Enhancers	Liver	Liver
47	chr5:52091600-52091800	Enhancers	Fetal Lung	lung
48	chr5:52091600-52092000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:52091600-52092800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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