Variant report

Variant	rs17739727
Chromosome Location	chr6:27329788-27329789
allele	A/C
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	JUND	chr6:27329553-27330210	SK-N-SH	brain:	n/a	n/a
2	JUN	chr6:27329689-27329998	HepG2	liver:	n/a	chr6:27329865-27329878
3	JUND	chr6:27329686-27330051	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27322944..27325251-chr6:27328933..27331710,2	K562	blood:
2	chr6:27329089..27331071-chr6:27332328..27335168,2	MCF-7	breast:

Variant related genes	Relation type
ZNF204P	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1127574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555040	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16867857	0.88[JPT][hapmap]
rs17688516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17739310	0.84[CHD][hapmap]
rs17739702	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2064092	0.81[CHD][hapmap];0.89[JPT][hapmap]
rs4145206	0.84[CHD][hapmap]
rs55923531	0.88[ASN][1000 genomes]
rs56388125	0.81[ASN][1000 genomes]
rs62622793	0.96[ASN][1000 genomes]
rs721600	0.92[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs72839482	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs764285	0.83[ASN][1000 genomes]
rs9348760	0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs9348761	0.94[TSI][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs9348762	0.84[EUR][1000 genomes]
rs9368502	0.94[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs9379976	0.86[TSI][hapmap]
rs9379977	0.86[TSI][hapmap]
rs9379978	0.94[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs9393805	0.86[TSI][hapmap]
rs9393807	0.87[YRI][hapmap]
rs9393808	0.94[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs9461357	0.84[CHD][hapmap]
rs9461359	0.82[EUR][1000 genomes]
rs9461360	0.82[EUR][1000 genomes]
rs9461362	0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[ASN][1000 genomes]
rs9461363	0.86[ASN][1000 genomes]
rs9461366	0.83[ASN][1000 genomes]
rs9468047	0.82[YRI][hapmap]
rs9468067	0.84[CHD][hapmap]
rs9468068	0.85[YRI][hapmap]
rs9468069	0.82[EUR][1000 genomes]
rs9468076	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468149	0.90[CHD][hapmap];0.89[JPT][hapmap]
rs9468152	0.89[JPT][hapmap]
rs9468153	0.89[JPT][hapmap]
rs9468155	0.89[JPT][hapmap]
rs9468159	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17739727	ZNF391	cis	cerebellum	SCAN
rs17739727	ZNF204P	cis	cerebellum	SCAN
rs17739727	HIST1H2AC	cis	parietal	SCAN
rs17739727	BTN3A3	cis	cerebellum	SCAN
rs17739727	HIST1H2AK	cis	parietal	SCAN
rs17739727	HIST1H3H	cis	cerebellum	SCAN
rs17739727	HIST1H2AL	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27316800-27335400	Weak transcription	Pancreas	Pancrea
2	chr6:27325800-27336200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:27326000-27331200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
4	chr6:27326000-27335600	Weak transcription	Brain Germinal Matrix	brain
5	chr6:27326200-27331000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:27326400-27331800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:27326800-27330800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
8	chr6:27326800-27331200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:27326800-27342000	Weak transcription	Colonic Mucosa	Colon
10	chr6:27327000-27332000	Weak transcription	Stomach Mucosa	stomach
11	chr6:27327000-27342000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:27327400-27330200	Weak transcription	Brain Anterior Caudate	brain
13	chr6:27327400-27333400	Weak transcription	Aorta	Aorta
14	chr6:27327400-27335600	Weak transcription	Gastric	stomach
15	chr6:27327400-27335800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:27327400-27336600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:27327400-27341800	Weak transcription	Fetal Brain Male	brain
18	chr6:27327400-27341800	Weak transcription	Fetal Kidney	kidney
19	chr6:27327600-27329800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:27327600-27335800	Weak transcription	Brain Angular Gyrus	brain
21	chr6:27327600-27342200	Weak transcription	Brain Substantia Nigra	brain
22	chr6:27327800-27329800	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr6:27328000-27335600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:27328000-27342400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:27328200-27330200	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:27328200-27330600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr6:27328200-27335800	Weak transcription	Right Ventricle	heart
28	chr6:27328200-27341800	Weak transcription	Adipose Nuclei	Adipose
29	chr6:27328200-27341800	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:27328200-27341800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr6:27328200-27342200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:27328400-27335200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:27328400-27341800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr6:27328600-27330200	Strong transcription	Left Ventricle	heart
35	chr6:27328800-27331200	Strong transcription	Fetal Lung	lung
36	chr6:27328800-27331200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr6:27328800-27331200	Strong transcription	Stomach Smooth Muscle	stomach
38	chr6:27328800-27331600	Strong transcription	Ovary	ovary
39	chr6:27329000-27331200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:27329200-27335600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr6:27329400-27335400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr6:27329400-27337000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr6:27329400-27341800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr6:27329600-27329800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
45	chr6:27329600-27329800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:27329600-27330600	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:27329600-27331200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr6:27329600-27335600	Weak transcription	Lung	lung

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