Variant report

Variant	rs1638703
Chromosome Location	chr13:51088356-51088357
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:51085819..51089100-chr13:51090794..51093089,4	K562	blood:
2	chr13:51087212..51089990-chr13:51483181..51484978,2	K562	blood:
3	chr13:50569721..50571547-chr13:51085881..51088680,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233672	Chromatin interaction
ENSG00000136104	Chromatin interaction
ENSG00000204977	Chromatin interaction
ENSG00000264864	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11618527	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12584983	0.81[CHB][hapmap]
rs1262775	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1262776	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1262778	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1262779	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1262780	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1327653	0.84[AFR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs149889	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs157164	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs157165	0.85[EUR][1000 genomes]
rs157166	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs157167	0.88[ASN][1000 genomes]
rs157169	0.91[ASN][1000 genomes]
rs157173	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1626445	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1630605	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17074530	0.80[ASN][1000 genomes]
rs1752106	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1752107	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1753633	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1753639	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs183949	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs183950	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs201748	0.81[ASN][1000 genomes]
rs201754	0.83[EUR][1000 genomes]
rs201757	0.85[EUR][1000 genomes]
rs201762	0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs202346	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs202347	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs202348	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2286658	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2429562	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3116598	0.82[EUR][1000 genomes]
rs3116599	0.81[TSI][hapmap]
rs3116600	0.80[EUR][1000 genomes]
rs3116601	0.80[EUR][1000 genomes]
rs3118903	0.83[EUR][1000 genomes]
rs3118909	0.80[EUR][1000 genomes]
rs495838	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs616268	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs975319	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs987086	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	nsv1045237	chr13:50976560-51102386	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1040	chr13:51041591-51090903	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1835159	chr13:51061044-51091390	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv1815534	chr13:51061044-51092946	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv1816672	chr13:51061044-51092946	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv1830736	chr13:51061044-51092946	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv1834352	chr13:51061044-51092946	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv1841390	chr13:51061044-51092946	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	esv1843375	chr13:51061044-51092946	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1638703	LPAR6	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51084200-51093200	Weak transcription	Spleen	Spleen
2	chr13:51084400-51093000	Weak transcription	Lung	lung
3	chr13:51085600-51089200	Enhancers	Fetal Intestine Small	intestine
4	chr13:51086200-51093000	Weak transcription	Placenta	Placenta
5	chr13:51086400-51092400	Weak transcription	Pancreas	Pancrea
6	chr13:51086800-51089200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr13:51086800-51089200	Enhancers	Fetal Intestine Large	intestine
8	chr13:51087000-51088800	Weak transcription	Aorta	Aorta
9	chr13:51087000-51089200	Enhancers	Primary hematopoietic stem cells	blood
10	chr13:51087000-51089200	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr13:51087000-51089400	Enhancers	Fetal Thymus	thymus
12	chr13:51087200-51088400	Enhancers	Primary B cells from peripheral blood	blood
13	chr13:51087200-51088600	Enhancers	Colon Smooth Muscle	Colon
14	chr13:51087200-51088600	Enhancers	Fetal Muscle Leg	muscle
15	chr13:51087200-51088600	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr13:51087200-51089200	Enhancers	Fetal Lung	lung
17	chr13:51087200-51089400	Enhancers	Thymus	Thymus
18	chr13:51087200-51092200	Weak transcription	Brain Angular Gyrus	brain
19	chr13:51087200-51095400	Weak transcription	Right Ventricle	heart
20	chr13:51087400-51088400	Enhancers	Brain Anterior Caudate	brain
21	chr13:51087400-51088400	Enhancers	Brain Substantia Nigra	brain
22	chr13:51087400-51089000	Enhancers	Fetal Heart	heart
23	chr13:51087400-51089200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr13:51087600-51088600	Enhancers	HepG2	liver
25	chr13:51087600-51089400	Enhancers	Dnd41	blood
26	chr13:51087600-51092200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr13:51087600-51092400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr13:51087600-51092400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr13:51087600-51093000	Weak transcription	Psoas Muscle	Psoas
30	chr13:51087600-51094800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr13:51087600-51095200	Weak transcription	Small Intestine	intestine
32	chr13:51087600-51095600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr13:51087800-51088400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr13:51087800-51088400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr13:51087800-51089000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr13:51087800-51089200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr13:51087800-51092400	Weak transcription	NHLF	lung
38	chr13:51087800-51092400	Weak transcription	Osteobl	bone
39	chr13:51087800-51092800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr13:51087800-51093000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr13:51087800-51093200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr13:51087800-51102000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr13:51088000-51088600	Enhancers	Liver	Liver
44	chr13:51088000-51088600	Weak transcription	Colonic Mucosa	Colon
45	chr13:51088000-51088800	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr13:51088000-51089200	Weak transcription	NHDF-Ad	bronchial
47	chr13:51088000-51090800	Weak transcription	Fetal Kidney	kidney
48	chr13:51088000-51091000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr13:51088000-51091000	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr13:51088000-51091800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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