Variant report

Variant	rs6467159
Chromosome Location	chr7:127742174-127742175
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127740635..127743022-chr7:127746178..127748843,2	MCF-7	breast:
2	chr7:127720893..127723705-chr7:127740814..127742874,2	K562	blood:
3	chr7:127737543..127740197-chr7:127740336..127742903,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207588	Chromatin interaction

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];0.98[ASN][1000 genomes]
rs322791	0.80[AFR][1000 genomes]
rs322806	0.80[AFR][1000 genomes]
rs322807	0.80[AFR][1000 genomes]
rs322808	0.80[AFR][1000 genomes]
rs322811	0.80[AFR][1000 genomes]
rs322812	0.88[LWK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs35045093	0.88[EUR][1000 genomes]
rs35361134	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4731395	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62484016	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6467160	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];1.00[ASN][1000 genomes]
rs6467163	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6953698	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954161	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954389	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs759710	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780024	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793071	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803045	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803473	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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];0.92[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs6467159	LRRC4	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127707800-127742200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr7:127724600-127743600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr7:127726000-127743600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr7:127730000-127742800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:127730400-127743800	Weak transcription	HSMM	muscle
6	chr7:127731400-127743600	Weak transcription	Brain Substantia Nigra	brain
7	chr7:127731800-127743600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:127732200-127743600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr7:127732800-127743600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:127733200-127743600	Weak transcription	Primary B cells from cord blood	blood
11	chr7:127733200-127743800	Weak transcription	Small Intestine	intestine
12	chr7:127733600-127743400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr7:127733600-127743600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr7:127733800-127743400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr7:127734200-127743600	Weak transcription	NHDF-Ad	bronchial
16	chr7:127734400-127744000	Weak transcription	A549	lung
17	chr7:127734400-127748200	Weak transcription	Dnd41	blood
18	chr7:127734600-127743600	Weak transcription	Brain Hippocampus Middle	brain
19	chr7:127734600-127743600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:127734800-127743600	Weak transcription	Brain Anterior Caudate	brain
21	chr7:127734800-127743600	Weak transcription	HUVEC	blood vessel
22	chr7:127735000-127743600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr7:127735000-127743600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr7:127735200-127742400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr7:127735200-127743000	Weak transcription	Right Atrium	heart
26	chr7:127735800-127743600	Weak transcription	Ovary	ovary
27	chr7:127736200-127743600	Weak transcription	HMEC	breast
28	chr7:127736400-127742400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:127736400-127743600	Weak transcription	Esophagus	oesophagus
30	chr7:127736400-127743600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr7:127736600-127742600	Weak transcription	Right Ventricle	heart
32	chr7:127736800-127743400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:127737400-127743400	Weak transcription	Adipose Nuclei	Adipose
34	chr7:127737800-127742200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:127737800-127743600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr7:127738200-127743600	Weak transcription	GM12878-XiMat	blood
37	chr7:127738400-127742600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr7:127738600-127743400	Weak transcription	Osteobl	bone
39	chr7:127738800-127742200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:127738800-127743600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr7:127738800-127743600	Weak transcription	Liver	Liver
42	chr7:127739000-127743400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr7:127739000-127743600	Weak transcription	Lung	lung
44	chr7:127739200-127742600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr7:127739400-127742400	Weak transcription	Fetal Intestine Small	intestine
46	chr7:127739400-127742400	Weak transcription	Fetal Stomach	stomach
47	chr7:127739400-127743400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:127739600-127742400	Weak transcription	Fetal Intestine Large	intestine
49	chr7:127739800-127742200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr7:127739800-127743000	Weak transcription	NHEK	skin

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