Variant report

Variant	rs6467163
Chromosome Location	chr7:127743638-127743639
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12706825	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs322791	0.82[AFR][1000 genomes]
rs322806	0.82[AFR][1000 genomes]
rs322807	0.82[AFR][1000 genomes]
rs322808	0.82[AFR][1000 genomes]
rs322811	0.82[AFR][1000 genomes]
rs322812	0.88[LWK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs35045093	0.88[EUR][1000 genomes]
rs35361134	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4731395	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62484016	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6467159	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6467160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6467161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6467162	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6953698	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6954161	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6954389	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs759710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7780024	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7792971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7793071	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7803045	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7803473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7811971	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6467163	LRRC4	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127730400-127743800	Weak transcription	HSMM	muscle
2	chr7:127733200-127743800	Weak transcription	Small Intestine	intestine
3	chr7:127734400-127744000	Weak transcription	A549	lung
4	chr7:127734400-127748200	Weak transcription	Dnd41	blood
5	chr7:127740600-127743800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr7:127740600-127743800	Enhancers	Spleen	Spleen
7	chr7:127740800-127743800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr7:127741600-127743800	Weak transcription	Aorta	Aorta
9	chr7:127743400-127743800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr7:127743400-127743800	Active TSS	Brain Cingulate Gyrus	brain
11	chr7:127743400-127743800	Bivalent Enhancer	Fetal Thymus	thymus
12	chr7:127743400-127744000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr7:127743400-127744000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:127743400-127744000	Flanking Active TSS	Right Ventricle	heart
15	chr7:127743400-127744200	Flanking Active TSS	Primary B cells from peripheral blood	blood
16	chr7:127743400-127744400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:127743400-127744600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:127743400-127744800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
19	chr7:127743400-127744800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr7:127743400-127744800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr7:127743400-127745000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr7:127743400-127745000	Active TSS	Primary T cells from cord blood	blood
23	chr7:127743600-127743800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:127743600-127743800	Active TSS	Primary B cells from cord blood	blood
25	chr7:127743600-127743800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
26	chr7:127743600-127743800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr7:127743600-127743800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr7:127743600-127743800	Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr7:127743600-127743800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:127743600-127743800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr7:127743600-127743800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:127743600-127743800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr7:127743600-127743800	Enhancers	Brain Angular Gyrus	brain
34	chr7:127743600-127743800	Active TSS	Brain Hippocampus Middle	brain
35	chr7:127743600-127743800	Active TSS	Brain Substantia Nigra	brain
36	chr7:127743600-127743800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
37	chr7:127743600-127743800	Bivalent Enhancer	Fetal Intestine Large	intestine
38	chr7:127743600-127743800	Enhancers	Gastric	stomach
39	chr7:127743600-127743800	Enhancers	Placenta Amnion	Placenta Amnion
40	chr7:127743600-127743800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
41	chr7:127743600-127743800	Active TSS	Rectal Smooth Muscle	rectum
42	chr7:127743600-127743800	Flanking Active TSS	Right Atrium	heart
43	chr7:127743600-127743800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
44	chr7:127743600-127743800	Enhancers	GM12878-XiMat	blood
45	chr7:127743600-127743800	Active TSS	HepG2	liver
46	chr7:127743600-127743800	Flanking Active TSS	HMEC	breast
47	chr7:127743600-127743800	Bivalent/Poised TSS	NH-A	brain
48	chr7:127743600-127743800	Flanking Active TSS	Osteobl	bone
49	chr7:127743600-127744000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr7:127743600-127744000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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