Variant report

Variant	rs4367376
Chromosome Location	chr6:25398990-25398991
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25394649..25396533-chr6:25398062..25399864,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10456044	0.81[JPT][hapmap]
rs10807003	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11757140	0.82[JPT][hapmap]
rs13214013	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1328264	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs188542	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs215010	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs215012	0.86[JPT][hapmap]
rs215015	0.83[JPT][hapmap]
rs2182931	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2328880	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs716797	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9379761	0.82[JPT][hapmap]

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
rs4367376	LRRC16A	cis	Whole Blood	GTEx
rs4367376	LRRC16	cis	multi-tissue	Pritchard
rs4367376	LRRC16	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25377400-25410600	Weak transcription	Gastric	stomach
2	chr6:25383000-25403600	Weak transcription	Right Atrium	heart
3	chr6:25383600-25405000	Weak transcription	Fetal Intestine Small	intestine
4	chr6:25389400-25403600	Weak transcription	Thymus	Thymus
5	chr6:25390200-25399400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:25390200-25401800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:25390200-25405000	Weak transcription	Adipose Nuclei	Adipose
8	chr6:25390400-25401600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:25390400-25401600	Weak transcription	HMEC	breast
10	chr6:25390800-25399200	Weak transcription	Fetal Thymus	thymus
11	chr6:25391400-25403800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr6:25394400-25403600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr6:25396000-25403600	Weak transcription	Primary T cells from cord blood	blood
14	chr6:25396200-25403400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:25397400-25399000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:25397600-25399000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr6:25397600-25405600	Weak transcription	Stomach Mucosa	stomach
18	chr6:25397800-25399000	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr6:25397800-25399400	Weak transcription	Left Ventricle	heart
20	chr6:25397800-25401800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:25397800-25403600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:25397800-25403800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:25397800-25403800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:25397800-25404200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:25397800-25404400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:25397800-25404400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:25398000-25401800	Weak transcription	Aorta	Aorta
28	chr6:25398000-25403600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:25398000-25404200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:25398400-25399000	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr6:25398800-25399000	Enhancers	H9 Cell Line	embryonic stem cell
32	chr6:25398800-25399200	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr6:25398800-25399400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:25398800-25399600	Enhancers	Small Intestine	intestine
35	chr6:25398800-25401800	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links