Variant report

Variant	rs17336532
Chromosome Location	chr6:28543264-28543265
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28543041..28546521-chr6:28553899..28555966,3	K562	blood:
2	chr6:28535055..28538009-chr6:28541570..28543876,2	K562	blood:
3	chr6:28537910..28539578-chr6:28542732..28545368,2	MCF-7	breast:
4	chr6:28542784..28545360-chr6:28545429..28548690,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246350	Chromatin interaction
ENSG00000232040	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1005126	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs11963067	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13190937	0.82[CHB][hapmap];0.95[CHD][hapmap]
rs13196606	0.81[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap]
rs13215054	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13215804	0.82[CHB][hapmap]
rs13217047	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16894116	0.89[CEU][hapmap]
rs16901847	0.89[CEU][hapmap]
rs16901848	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2394102	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35051649	0.82[ASN][1000 genomes]
rs35257859	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35546888	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35778344	0.87[ASN][1000 genomes]
rs3799499	0.80[CEU][hapmap];0.84[CHD][hapmap]
rs3799500	0.82[CHB][hapmap]
rs41270599	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902687	0.81[CHB][hapmap]
rs6905380	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs6923110	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6941188	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7742957	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7754960	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs7766356	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs7774981	0.85[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][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	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs17336532	HIST1H2BH	cis	cerebellum	SCAN
rs17336532	ZNF323	cis	parietal	SCAN
rs17336532	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs17336532	HLA-H	cis	multi-tissue	Pritchard
rs17336532	ZSCAN23	cis	cerebellum	SCAN
rs17336532	ZFP57	cis	multi-tissue	Pritchard
rs17336532	HLA-A	cis	multi-tissue	Pritchard
rs17336532	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs17336532	ZNF192	cis	cerebellum	SCAN
rs17336532	HLA-G	cis	multi-tissue	Pritchard
rs17336532	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs17336532	BTN3A3	cis	parietal	SCAN
rs17336532	ZSCAN23	cis	parietal	SCAN
rs17336532	BTN3A2	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28531800-28553200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:28532000-28552600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:28535000-28554000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:28536600-28553200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:28537200-28543800	Weak transcription	GM12878-XiMat	blood
6	chr6:28537200-28553200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:28537200-28554000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:28537400-28553800	Weak transcription	Fetal Muscle Leg	muscle
9	chr6:28538800-28553000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:28539400-28552800	Weak transcription	Fetal Intestine Large	intestine
11	chr6:28540000-28549200	Weak transcription	Ovary	ovary
12	chr6:28540000-28554000	Weak transcription	Gastric	stomach
13	chr6:28540600-28544000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:28540600-28554200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:28540800-28543600	Strong transcription	Fetal Brain Female	brain
16	chr6:28541000-28554200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:28541200-28544200	Strong transcription	Brain Germinal Matrix	brain
18	chr6:28541400-28553200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:28541400-28554000	Weak transcription	Pancreas	Pancrea
20	chr6:28541600-28543800	Strong transcription	K562	blood
21	chr6:28542000-28543800	Strong transcription	Fetal Kidney	kidney
22	chr6:28542200-28544600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:28542200-28553200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:28542600-28553000	Weak transcription	Fetal Intestine Small	intestine
25	chr6:28542800-28543600	Strong transcription	HepG2	liver
26	chr6:28543200-28543800	Strong transcription	Liver	Liver
27	chr6:28543200-28547600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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