Variant report

Variant	rs11759648
Chromosome Location	chr6:25359637-25359638
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10456322	1.00[JPT][hapmap]
rs10456323	1.00[JPT][hapmap]
rs11752017	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11759560	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12154021	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12192331	1.00[JPT][hapmap]
rs12203031	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12203442	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12211739	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1410443	1.00[JPT][hapmap]
rs150533	1.00[JPT][hapmap]
rs184202	1.00[JPT][hapmap]
rs1880271	1.00[CHD][hapmap]
rs212927	1.00[JPT][hapmap]
rs212929	1.00[JPT][hapmap]
rs212931	1.00[JPT][hapmap]
rs212932	1.00[JPT][hapmap]
rs212935	1.00[JPT][hapmap]
rs212937	1.00[JPT][hapmap]
rs212939	1.00[JPT][hapmap]
rs212940	1.00[JPT][hapmap]
rs2690047	1.00[CHD][hapmap]
rs2690076	1.00[CHD][hapmap]
rs2690102	1.00[CHD][hapmap]
rs2690124	1.00[CHD][hapmap]
rs2744282	1.00[CHD][hapmap]
rs301377	1.00[JPT][hapmap]
rs441472	1.00[JPT][hapmap]
rs453181	1.00[JPT][hapmap]
rs485567	1.00[JPT][hapmap]
rs6927384	1.00[JPT][hapmap]
rs6931843	1.00[JPT][hapmap]
rs716796	1.00[JPT][hapmap]
rs760865	1.00[JPT][hapmap]
rs7752524	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7762537	1.00[JPT][hapmap]
rs7764258	1.00[JPT][hapmap]
rs940405	1.00[CHD][hapmap]
rs9461151	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs9467496	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11759648	LRRC16	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25335200-25359800	Weak transcription	Thymus	Thymus
2	chr6:25352200-25363000	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr6:25358200-25361000	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr6:25358800-25361400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:25358800-25362600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:25359000-25360000	Enhancers	Fetal Kidney	kidney
7	chr6:25359000-25360400	Enhancers	Brain Germinal Matrix	brain
8	chr6:25359000-25360800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr6:25359200-25359800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:25359200-25359800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:25359200-25360000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:25359200-25360000	Enhancers	H9 Cell Line	embryonic stem cell
13	chr6:25359200-25360000	Enhancers	Lung	lung
14	chr6:25359200-25360400	Enhancers	Stomach Mucosa	stomach
15	chr6:25359200-25360600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:25359200-25360600	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr6:25359200-25360800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:25359200-25361000	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr6:25359200-25361000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:25359200-25361000	Enhancers	Ovary	ovary
21	chr6:25359200-25361000	Enhancers	Small Intestine	intestine
22	chr6:25359200-25361000	Enhancers	A549	lung
23	chr6:25359200-25361200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr6:25359200-25361200	Enhancers	Duodenum Mucosa	Duodenum
25	chr6:25359200-25361200	Enhancers	HSMM	muscle
26	chr6:25359200-25361400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:25359200-25362800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:25359200-25363600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:25359400-25359800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr6:25359400-25359800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:25359400-25359800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:25359400-25359800	Enhancers	Brain Angular Gyrus	brain
33	chr6:25359400-25359800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr6:25359400-25359800	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
35	chr6:25359400-25359800	Enhancers	Fetal Muscle Trunk	muscle
36	chr6:25359400-25359800	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr6:25359400-25359800	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr6:25359400-25359800	Flanking Active TSS	Hela-S3	cervix
39	chr6:25359400-25359800	Flanking Active TSS	NHDF-Ad	bronchial
40	chr6:25359400-25360000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:25359400-25360000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr6:25359400-25360000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:25359400-25360000	Enhancers	Fetal Intestine Large	intestine
44	chr6:25359400-25360000	Enhancers	Right Atrium	heart
45	chr6:25359400-25360000	Flanking Active TSS	NH-A	brain
46	chr6:25359400-25360000	Flanking Active TSS	NHLF	lung
47	chr6:25359400-25360200	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr6:25359400-25360200	Flanking Active TSS	Fetal Lung	lung
49	chr6:25359400-25360200	Flanking Active TSS	HMEC	breast
50	chr6:25359400-25360400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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