Variant report

Variant	rs10867357
Chromosome Location	chr9:71939431-71939432
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	MAX	chr9:71939343-71940350	H1-hESC	embryonic stem cell:	n/a	chr9:71940260-71940269 chr9:71940289-71940299
2	HDAC2	chr9:71939415-71940308	MCF-7	breast:	n/a	n/a
3	POLR2A	chr9:71939400-71939911	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF143	chr9:71939413-71939798	H1-hESC	embryonic stem cell:	n/a	n/a
5	KAP1	chr9:71939400-71940134	HEK293	kidney:	n/a	chr9:71939736-71939744
6	MAX	chr9:71939215-71940286	HCT-116	colon:	n/a	chr9:71940260-71940269
7	MAX	chr9:71939328-71940369	H1-hESC	embryonic stem cell:	n/a	chr9:71940260-71940269 chr9:71940289-71940299
8	MAX	chr9:71939382-71939738	H1-hESC	embryonic stem cell:	n/a	n/a
9	SIN3A	chr9:71939340-71941514	H1-hESC	embryonic stem cell:	n/a	chr9:71939943-71939956 chr9:71940048-71940061
10	POLR2A	chr9:71939366-71939737	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr9:71939342-71939706	H1-neurons	neurons:	n/a	n/a
12	SIN3AK20	chr9:71939350-71939969	H1-hESC	embryonic stem cell:	n/a	n/a
13	MXI1	chr9:71939389-71940163	H1-hESC	embryonic stem cell:	n/a	n/a
14	EP300	chr9:71939316-71940840	ECC-1	luminal epithelium:	n/a	chr9:71940177-71940193 chr9:71940486-71940502 chr9:71940180-71940196 chr9:71940022-71940038
15	CHD1	chr9:71939130-71939630	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr9:71939352-71940273	H1-hESC	embryonic stem cell:	n/a	n/a
17	CREB1	chr9:71939374-71940226	H1-hESC	embryonic stem cell:	n/a	chr9:71939809-71939822
18	MAX	chr9:71939347-71940331	MCF-7	breast:	n/a	chr9:71940260-71940269 chr9:71940289-71940299
19	CHD2	chr9:71939386-71939672	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr9:71939176-71940373	H1-hESC	embryonic stem cell:	n/a	n/a
21	TAF1	chr9:71939341-71940245	H1-hESC	embryonic stem cell:	n/a	n/a
22	BRCA1	chr9:71939386-71939797	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr9:71939319-71940421	ECC-1	luminal epithelium:	n/a	chr9:71940260-71940269 chr9:71940289-71940299
24	TBP	chr9:71939336-71940217	H1-hESC	embryonic stem cell:	n/a	n/a
25	NANOG	chr9:71939401-71939843	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr9:71939328-71940693	H1-hESC	embryonic stem cell:	n/a	n/a
27	E2F6	chr9:71939292-71940238	H1-hESC	embryonic stem cell:	n/a	chr9:71939929-71939940 chr9:71940063-71940073
28	YY1	chr9:71939332-71939743	H1-hESC	embryonic stem cell:	n/a	chr9:71939434-71939445
29	MAX	chr9:71939334-71940305	HCT-116	colon:	n/a	chr9:71940260-71940269 chr9:71940289-71940299
30	E2F6	chr9:71939397-71939840	A549	lung:	n/a	n/a
31	RAD21	chr9:71939290-71940131	H1-hESC	embryonic stem cell:	n/a	chr9:71939998-71940012 chr9:71939996-71940010
32	TAF7	chr9:71939277-71940276	H1-hESC	embryonic stem cell:	n/a	n/a
33	JUND	chr9:71939401-71939988	H1-hESC	embryonic stem cell:	n/a	n/a
34	TEAD4	chr9:71939357-71939746	H1-hESC	embryonic stem cell:	n/a	n/a
35	ZNF263	chr9:71939402-71940751	HEK293-T-REx	kidney:	n/a	chr9:71940097-71940118
36	POLR2A	chr9:71939321-71940797	MCF-7	breast:	n/a	n/a
37	E2F6	chr9:71939189-71940270	H1-hESC	embryonic stem cell:	n/a	chr9:71939929-71939940 chr9:71940063-71940073
38	MAX	chr9:71939361-71940324	ECC-1	luminal epithelium:	n/a	chr9:71940260-71940269 chr9:71940289-71940299
39	TEAD4	chr9:71939367-71939745	H1-hESC	embryonic stem cell:	n/a	n/a
40	HA-E2F1	chr9:71939219-71940234	MCF-7	breast:	n/a	chr9:71939929-71939940 chr9:71940063-71940073

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71937269..71941011-chr9:72000572..72004392,4	MCF-7	breast:
2	chr9:71938510..71941284-chr9:71942079..71947019,4	MCF-7	breast:

Variant related genes	Relation type
FAM189A2	TF binding region
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10780308	0.82[CHD][hapmap]
rs10867360	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10867367	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11791211	0.86[ASN][1000 genomes]
rs13292207	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1339544	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[ASN][1000 genomes]
rs1962383	0.81[AMR][1000 genomes]
rs3750552	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4382537	0.82[CHD][hapmap]
rs4515616	0.80[CHD][hapmap]
rs4744566	0.82[CHD][hapmap]
rs4744881	0.82[CHD][hapmap]
rs6559468	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6559472	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7027671	0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs7044101	0.82[CHB][hapmap]
rs7852930	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3374800	chr9:71939157-71942005	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3417138	chr9:71939382-71941480	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10867357	TJP2	cis	parietal	SCAN
rs10867357	C9orf57	cis	cerebellum	SCAN
rs10867357	FAM189A2	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71937600-71942800	Active TSS	Fetal Heart	heart
2	chr9:71938800-71940800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr9:71938800-71940800	Active TSS	Brain Substantia Nigra	brain
4	chr9:71938800-71941400	Active TSS	Brain Anterior Caudate	brain
5	chr9:71938800-71942800	Active TSS	Right Atrium	heart
6	chr9:71939000-71940600	Bivalent/Poised TSS	Fetal Lung	lung
7	chr9:71939000-71940800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
8	chr9:71939000-71941000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr9:71939000-71941000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr9:71939000-71941200	Active TSS	Ovary	ovary
11	chr9:71939000-71941400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr9:71939000-71942800	Active TSS	Stomach Smooth Muscle	stomach
13	chr9:71939200-71939600	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:71939200-71939600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr9:71939200-71939800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr9:71939200-71940000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
17	chr9:71939200-71940600	Active TSS	Brain Hippocampus Middle	brain
18	chr9:71939200-71940600	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr9:71939200-71940800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
20	chr9:71939200-71940800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:71939200-71941000	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr9:71939200-71941200	Active TSS	H9 Cell Line	embryonic stem cell
23	chr9:71939200-71941400	Active TSS	Left Ventricle	heart
24	chr9:71939200-71944000	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr9:71939400-71939600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:71939400-71939600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:71939400-71939600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
28	chr9:71939400-71939600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:71939400-71939600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
30	chr9:71939400-71939600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr9:71939400-71939600	Flanking Bivalent TSS/Enh	Liver	Liver
32	chr9:71939400-71939600	Flanking Active TSS	Brain Angular Gyrus	brain
33	chr9:71939400-71939600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
34	chr9:71939400-71939600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:71939400-71939600	Active TSS	Colonic Mucosa	Colon
36	chr9:71939400-71939600	Flanking Active TSS	Pancreas	Pancrea
37	chr9:71939400-71939600	Flanking Bivalent TSS/Enh	Placenta Amnion	Placenta Amnion
38	chr9:71939400-71939600	Flanking Bivalent TSS/Enh	Rectal Smooth Muscle	rectum
39	chr9:71939400-71939600	Flanking Bivalent TSS/Enh	Stomach Mucosa	stomach
40	chr9:71939400-71939600	Active TSS	Spleen	Spleen
41	chr9:71939400-71939600	Flanking Bivalent TSS/Enh	HSMMtube	muscle
42	chr9:71939400-71939600	Bivalent/Poised TSS	NHLF	lung
43	chr9:71939400-71939600	Bivalent/Poised TSS	Osteobl	bone
44	chr9:71939400-71939800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
45	chr9:71939400-71939800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:71939400-71939800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:71939400-71939800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
48	chr9:71939400-71939800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
49	chr9:71939400-71939800	Flanking Bivalent TSS/Enh	Placenta	Placenta
50	chr9:71939400-71939800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links