Variant report

Variant	rs6924540
Chromosome Location	chr6:25404749-25404750
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10946771	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10946772	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10946773	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10946774	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10946775	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10946776	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12662331	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12662334	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2328883	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2328884	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56125342	0.82[ASN][1000 genomes]
rs6919767	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6937918	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6938645	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7341239	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7341240	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs880226	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs881696	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs881697	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295656	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461154	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461155	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461156	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461157	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461158	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461160	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461161	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461162	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461163	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461164	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461165	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9467483	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467484	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467485	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467486	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467487	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467488	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467489	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467490	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467491	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9467492	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467493	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9467494	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9467499	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9467500	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9467502	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9467503	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs985985	0.80[AMR][1000 genomes];0.99[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6924540	LRRC16A	cis	Whole Blood	GTEx
rs6924540	LRRC16	Cis_1M	lymphoblastoid	RTeQTL

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	chr6:25402200-25405000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:25402200-25405000	Weak transcription	NHEK	skin
8	chr6:25402200-25405200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr6:25402200-25405200	Weak transcription	HMEC	breast
10	chr6:25402200-25406200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:25402200-25409600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:25402400-25405000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:25403200-25404800	Enhancers	Primary B cells from peripheral blood	blood
14	chr6:25403400-25404800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:25403400-25404800	Enhancers	Fetal Thymus	thymus
16	chr6:25403400-25405000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:25403600-25404800	Enhancers	Thymus	Thymus
18	chr6:25403600-25405000	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr6:25403600-25405000	Enhancers	Primary B cells from cord blood	blood
20	chr6:25403600-25405000	Enhancers	Primary T cells fromperipheralblood	blood
21	chr6:25403600-25405000	Enhancers	Primary hematopoietic stem cells	blood
22	chr6:25403600-25405000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:25403600-25405000	Enhancers	Duodenum Mucosa	Duodenum
24	chr6:25403600-25405200	Enhancers	Lung	lung
25	chr6:25403600-25405200	Enhancers	Right Atrium	heart
26	chr6:25403600-25405200	Enhancers	Small Intestine	intestine
27	chr6:25403600-25406000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:25403600-25406400	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr6:25403600-25408200	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr6:25403800-25404800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr6:25403800-25405000	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr6:25403800-25405000	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr6:25403800-25405200	Enhancers	H1 Cell Line	embryonic stem cell
34	chr6:25403800-25406000	Enhancers	Brain Substantia Nigra	brain
35	chr6:25403800-25406400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr6:25403800-25406400	Weak transcription	Spleen	Spleen
37	chr6:25403800-25410600	Weak transcription	Pancreas	Pancrea
38	chr6:25404000-25405000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr6:25404000-25405000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:25404000-25405000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr6:25404200-25404800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr6:25404200-25405000	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr6:25404200-25405200	Active TSS	Rectal Smooth Muscle	rectum
44	chr6:25404200-25406000	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr6:25404400-25404800	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr6:25404400-25404800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr6:25404400-25404800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr6:25404400-25404800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:25404400-25404800	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr6:25404400-25405000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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