Variant report

Variant	rs6919767
Chromosome Location	chr6:25404499-25404500
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10946771	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946773	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946774	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946775	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10946776	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12662331	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662334	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328883	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56125342	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6924540	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6937918	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6938645	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7341239	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7341240	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs880226	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881697	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295656	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461154	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461155	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461156	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461157	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461158	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461160	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461161	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461162	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461163	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461164	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461165	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9467483	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467484	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467485	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467486	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467487	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467488	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467489	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467490	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467491	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9467492	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9467493	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467494	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467499	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467500	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467502	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467503	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs985985	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6919767	LRRC16	Cis_1M	lymphoblastoid	RTeQTL
rs6919767	LRRC16	cis	multi-tissue	Pritchard
rs6919767	LRRC16A	cis	Whole Blood	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25377400-25410600	Weak transcription	Gastric	stomach
2	chr6:25383600-25405000	Weak transcription	Fetal Intestine Small	intestine
3	chr6:25390200-25405000	Weak transcription	Adipose Nuclei	Adipose
4	chr6:25397600-25405600	Weak transcription	Stomach Mucosa	stomach
5	chr6:25399000-25405200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:25402200-25404600	Weak transcription	Aorta	Aorta
7	chr6:25402200-25405000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:25402200-25405000	Weak transcription	NHEK	skin
9	chr6:25402200-25405200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:25402200-25405200	Weak transcription	HMEC	breast
11	chr6:25402200-25406200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:25402200-25409600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:25402400-25405000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:25403200-25404600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:25403200-25404800	Enhancers	Primary B cells from peripheral blood	blood
16	chr6:25403400-25404800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:25403400-25404800	Enhancers	Fetal Thymus	thymus
18	chr6:25403400-25405000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:25403600-25404800	Enhancers	Thymus	Thymus
20	chr6:25403600-25405000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr6:25403600-25405000	Enhancers	Primary B cells from cord blood	blood
22	chr6:25403600-25405000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr6:25403600-25405000	Enhancers	Primary hematopoietic stem cells	blood
24	chr6:25403600-25405000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:25403600-25405000	Enhancers	Duodenum Mucosa	Duodenum
26	chr6:25403600-25405200	Enhancers	Lung	lung
27	chr6:25403600-25405200	Enhancers	Right Atrium	heart
28	chr6:25403600-25405200	Enhancers	Small Intestine	intestine
29	chr6:25403600-25406000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr6:25403600-25406400	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr6:25403600-25408200	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr6:25403800-25404600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr6:25403800-25404800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr6:25403800-25405000	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr6:25403800-25405000	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr6:25403800-25405200	Enhancers	H1 Cell Line	embryonic stem cell
37	chr6:25403800-25406000	Enhancers	Brain Substantia Nigra	brain
38	chr6:25403800-25406400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:25403800-25406400	Weak transcription	Spleen	Spleen
40	chr6:25403800-25410600	Weak transcription	Pancreas	Pancrea
41	chr6:25404000-25405000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:25404000-25405000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:25404000-25405000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:25404200-25404600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr6:25404200-25404800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:25404200-25405000	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr6:25404200-25405200	Active TSS	Rectal Smooth Muscle	rectum
48	chr6:25404200-25406000	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr6:25404400-25404600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr6:25404400-25404600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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