Variant report

Variant	rs8079359
Chromosome Location	chr17:38641505-38641506
allele	A/G
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	USF2	chr17:38640614-38644462	Hela-S3	cervix:	n/a	n/a
2	SP1	chr17:38641487-38644341	A549	lung:	n/a	chr17:38643833-38643843 chr17:38641746-38641760 chr17:38643834-38643843 chr17:38642241-38642250 chr17:38642240-38642250 chr17:38642239-38642251
3	POLR2A	chr17:38637848-38650725	A549	lung:	n/a	n/a
4	POLR2A	chr17:38639722-38641776	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr17:38639013-38641604	Hela-S3	cervix:	n/a	n/a
6	BCL3	chr17:38639720-38643973	A549	lung:	n/a	n/a
7	SP1	chr17:38641347-38643891	A549	lung:	n/a	chr17:38643833-38643843 chr17:38641746-38641760 chr17:38643834-38643843 chr17:38642241-38642250 chr17:38642240-38642250 chr17:38642239-38642251
8	POLR2A	chr17:38639824-38641744	Hela-S3	cervix:	n/a	n/a
9	MAZ	chr17:38641397-38643919	IMR90	lung:	n/a	chr17:38642317-38642327 chr17:38643796-38643805
10	SIX5	chr17:38640768-38644658	A549	lung:	n/a	chr17:38642468-38642477
11	POLR2A	chr17:38638883-38645646	MCF10A-Er-Src	breast:	n/a	n/a
12	BCL3	chr17:38639648-38644407	A549	lung:	n/a	n/a
13	ATF3	chr17:38641488-38643532	A549	lung:	n/a	n/a
14	POLR2A	chr17:38641013-38643731	IMR90	lung:	n/a	n/a
15	TCF12	chr17:38639929-38641563	A549	lung:	n/a	n/a
16	MAX	chr17:38641446-38645160	A549	lung:	n/a	chr17:38642317-38642327 chr17:38643796-38643805
17	POLR2A	chr17:38638060-38645729	MCF10A-Er-Src	breast:	n/a	n/a
18	GATA3	chr17:38641480-38644133	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38640900..38643857-chr17:38669358..38670867,2	MCF-7	breast:
2	chr17:38639003..38641951-chr17:38683883..38685651,2	MCF-7	breast:
3	chr17:38640893..38644463-chr17:38672113..38675330,4	MCF-7	breast:
4	chr17:38641070..38642777-chr17:38643354..38644884,2	K562	blood:
5	chr17:38633817..38637978-chr17:38639202..38643004,3	K562	blood:
6	chr17:38640863..38643911-chr17:38644729..38647819,3	MCF-7	breast:
7	chr15:74218995..74221163-chr17:38641031..38642876,2	MCF-7	breast:
8	chr17:38640622..38642550-chr17:38663803..38666620,2	K562	blood:
9	chr17:38638255..38640177-chr17:38640329..38642532,3	K562	blood:
10	chr17:38640983..38649598-chr17:38652430..38659338,11	MCF-7	breast:
11	chr17:38634038..38637576-chr17:38640830..38643969,3	MCF-7	breast:
12	chr17:38639539..38641673-chr17:38677366..38679503,2	K562	blood:

Variant related genes	Relation type
TNS4	TF binding region
ENSG00000131746	Chromatin interaction
ENSG00000261801	Chromatin interaction
ENSG00000266088	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11078948	0.84[ASN][1000 genomes]
rs1666263	0.89[CHB][hapmap]
rs17557153	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs1901187	0.82[ASW][hapmap];0.92[LWK][hapmap];0.91[MKK][hapmap];0.82[AFR][1000 genomes]
rs2122614	0.82[ASN][1000 genomes]
rs627857	1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs9303289	0.82[AFR][1000 genomes]

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	nsv1058185	chr17:38629339-38689908	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv908224	chr17:38638251-38651447	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8079359	KRT36	cis	cerebellum	SCAN
rs8079359	CCL13	cis	cerebellum	SCAN
rs8079359	TCAP	cis	cerebellum	SCAN
rs8079359	KRT16	cis	cerebellum	SCAN
rs8079359	C17orf50	cis	parietal	SCAN
rs8079359	SLFN13	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38627400-38646200	Weak transcription	Gastric	stomach
2	chr17:38633400-38643800	Weak transcription	Right Ventricle	heart
3	chr17:38635800-38641800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr17:38636000-38647000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr17:38636000-38648200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr17:38636000-38649600	Genic enhancers	HMEC	breast
7	chr17:38636600-38642600	Weak transcription	Right Atrium	heart
8	chr17:38636800-38642000	Genic enhancers	Hela-S3	cervix
9	chr17:38637000-38643400	Enhancers	K562	blood
10	chr17:38637000-38644800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr17:38637200-38642000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr17:38637400-38642000	Strong transcription	Placenta	Placenta
13	chr17:38637400-38642200	Weak transcription	Adipose Nuclei	Adipose
14	chr17:38637400-38642400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr17:38637400-38642800	Weak transcription	Small Intestine	intestine
16	chr17:38637400-38645600	Weak transcription	Spleen	Spleen
17	chr17:38637400-38648200	Genic enhancers	NHEK	skin
18	chr17:38637600-38642200	Weak transcription	Fetal Thymus	thymus
19	chr17:38637600-38642600	Weak transcription	Esophagus	oesophagus
20	chr17:38638200-38642800	Weak transcription	Primary T cells from cord blood	blood
21	chr17:38638200-38646400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr17:38638400-38643200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr17:38638600-38642200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr17:38638600-38646200	Weak transcription	Colonic Mucosa	Colon
25	chr17:38638800-38642600	Weak transcription	Lung	lung
26	chr17:38638800-38646000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr17:38639200-38642600	Weak transcription	Stomach Mucosa	stomach
28	chr17:38639200-38645000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr17:38639200-38645000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr17:38639200-38645400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr17:38639200-38645400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr17:38639400-38643200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr17:38639400-38644400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr17:38639400-38645400	Weak transcription	Primary B cells from cord blood	blood
35	chr17:38639600-38641600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr17:38639600-38641800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr17:38639600-38644200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr17:38639800-38641800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr17:38639800-38642000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr17:38639800-38643400	Enhancers	HepG2	liver
41	chr17:38639800-38644200	Enhancers	Placenta Amnion	Placenta Amnion
42	chr17:38640000-38641600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr17:38640000-38643200	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr17:38640200-38642800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr17:38640400-38641600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr17:38640400-38643400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr17:38640600-38641600	Enhancers	Muscle Satellite Cultured Cells	--
48	chr17:38640800-38641800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr17:38640800-38643400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr17:38640800-38644400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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