Variant report

Variant	rs985984
Chromosome Location	chr6:25402179-25402180
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11967836	0.82[CEU][hapmap]
rs17251430	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17316893	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17677216	1.00[ASN][1000 genomes]
rs17677373	1.00[ASN][1000 genomes]
rs17734132	1.00[ASN][1000 genomes]
rs17734186	1.00[ASN][1000 genomes]
rs1883392	0.82[CEU][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap]
rs2149227	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6456671	0.82[CEU][hapmap]
rs6939174	1.00[ASN][1000 genomes]
rs7748771	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs9467477	0.80[EUR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs985984	HIST1H3D	cis	lymphoblastoid	seeQTL
rs985984	ARMCX5	trans	lymphoblastoid	seeQTL
rs985984	HIST1H2AE	cis	lymphoblastoid	seeQTL
rs985984	HIST1H2BC	cis	lymphoblastoid	seeQTL
rs985984	HIST1H2AD	cis	lymphoblastoid	seeQTL

Chromatin state (count:37 , 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	chr6:25390200-25405000	Weak transcription	Adipose Nuclei	Adipose
6	chr6:25391400-25403800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr6:25394400-25403600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr6:25396000-25403600	Weak transcription	Primary T cells from cord blood	blood
9	chr6:25396200-25403400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:25397600-25405600	Weak transcription	Stomach Mucosa	stomach
11	chr6:25397800-25403600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:25397800-25403800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:25397800-25403800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr6:25397800-25404200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:25397800-25404400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:25397800-25404400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:25398000-25403600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr6:25398000-25404200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr6:25399000-25403600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:25399000-25404200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:25399000-25405200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:25399200-25404400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:25399400-25403600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:25399600-25403400	Weak transcription	Fetal Thymus	thymus
25	chr6:25399600-25403600	Weak transcription	Small Intestine	intestine
26	chr6:25400000-25402200	Enhancers	NHEK	skin
27	chr6:25400800-25402200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:25401600-25402200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr6:25401600-25402200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr6:25401600-25402200	Enhancers	HMEC	breast
31	chr6:25401800-25402200	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr6:25401800-25402200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:25401800-25402200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:25401800-25402200	Enhancers	Aorta	Aorta
35	chr6:25401800-25402400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:25402000-25402200	Enhancers	Spleen	Spleen
37	chr6:25402000-25404400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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