Variant report

Variant	rs9461160
Chromosome Location	chr6:25404970-25404971
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:25404920-25405392	GM12892	blood:	n/a	n/a
2	ELF1	chr6:25404961-25405373	GM12878	blood:	n/a	n/a
3	PAX5	chr6:25404931-25405330	GM12878	blood:	n/a	chr6:25405260-25405269 chr6:25405263-25405272
4	MTA3	chr6:25404914-25405788	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:25404911-25405477	GM12892	blood:	n/a	n/a
6	YY1	chr6:25404878-25405323	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:25404964-25405424	GM12878	blood:	n/a	n/a
8	NFATC1	chr6:25404941-25405472	GM12878	blood:	n/a	n/a
9	RUNX3	chr6:25404912-25405434	GM12878	blood:	n/a	n/a
10	POU2F2	chr6:25404927-25405438	GM12878	blood:	n/a	n/a
11	NFIC	chr6:25404897-25406001	GM12878	blood:	n/a	n/a
12	ATF2	chr6:25404958-25405638	GM12878	blood:	n/a	n/a
13	PAX5	chr6:25404937-25405472	GM12878	blood:	n/a	chr6:25405260-25405269 chr6:25405263-25405272
14	IRF4	chr6:25404923-25405530	GM12878	blood:	n/a	n/a
15	PML	chr6:25404914-25405879	GM12878	blood:	n/a	n/a
16	FOXM1	chr6:25404944-25405595	GM12878	blood:	n/a	n/a
17	IRF4	chr6:25404914-25405466	GM12878	blood:	n/a	n/a
18	RUNX3	chr6:25404863-25406226	GM12878	blood:	n/a	n/a
19	CEBPB	chr6:25404965-25405641	GM12878	blood:	n/a	n/a
20	ZNF384	chr6:25404872-25405406	GM12878	blood:	n/a	n/a
21	NFIC	chr6:25404889-25406187	GM12878	blood:	n/a	n/a
22	SPI1	chr6:25404772-25406213	GM12878	blood:	n/a	chr6:25405260-25405269 chr6:25405801-25405810 chr6:25405835-25405848 chr6:25405838-25405847 chr6:25405836-25405849

Variant related genes	Relation type
ENSG00000253017	TF binding region

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

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

rs_ID	r²[population]
rs10946771	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946772	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946773	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946774	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946775	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10946776	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12662331	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662334	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328883	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328884	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56125342	0.83[ASN][1000 genomes]
rs6919767	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924540	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6937918	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6938645	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7341239	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7341240	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs880226	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881696	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881697	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295656	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461154	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461155	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461156	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461157	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461158	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461161	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461162	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461163	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461164	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461165	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9467483	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467484	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467485	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467486	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467487	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467488	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467489	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467490	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467491	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9467492	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9467493	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467494	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467499	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467500	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467502	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467503	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs985985	0.82[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9461160	LRRC16	Cis_1M	lymphoblastoid	RTeQTL
rs9461160	LRRC16A	cis	Whole Blood	GTEx

Chromatin state (count:68 , 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	chr6:25403400-25405000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:25403600-25405000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:25403600-25405000	Enhancers	Primary B cells from cord blood	blood
16	chr6:25403600-25405000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr6:25403600-25405000	Enhancers	Primary hematopoietic stem cells	blood
18	chr6:25403600-25405000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:25403600-25405000	Enhancers	Duodenum Mucosa	Duodenum
20	chr6:25403600-25405200	Enhancers	Lung	lung
21	chr6:25403600-25405200	Enhancers	Right Atrium	heart
22	chr6:25403600-25405200	Enhancers	Small Intestine	intestine
23	chr6:25403600-25406000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:25403600-25406400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr6:25403600-25408200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr6:25403800-25405000	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr6:25403800-25405000	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr6:25403800-25405200	Enhancers	H1 Cell Line	embryonic stem cell
29	chr6:25403800-25406000	Enhancers	Brain Substantia Nigra	brain
30	chr6:25403800-25406400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:25403800-25406400	Weak transcription	Spleen	Spleen
32	chr6:25403800-25410600	Weak transcription	Pancreas	Pancrea
33	chr6:25404000-25405000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr6:25404000-25405000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:25404000-25405000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:25404200-25405000	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr6:25404200-25405200	Active TSS	Rectal Smooth Muscle	rectum
38	chr6:25404200-25406000	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr6:25404400-25405000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:25404400-25405200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:25404400-25405200	Enhancers	Fetal Muscle Leg	muscle
42	chr6:25404400-25406400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr6:25404400-25406600	Enhancers	Colonic Mucosa	Colon
44	chr6:25404400-25406600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr6:25404400-25407400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:25404400-25407600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr6:25404400-25410800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:25404600-25405000	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr6:25404600-25405000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:25404600-25405000	Enhancers	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links