Variant report

Variant	rs9700179
Chromosome Location	chr1:153585584-153585585
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	POLR2A	chr1:153578781-153585928	U87	brain:	n/a	n/a
2	POLR2A	chr1:153585302-153585644	A549	lung:	n/a	n/a
3	POLR2A	chr1:153580416-153585950	Hela-S3	cervix:	n/a	n/a
4	MAZ	chr1:153583230-153586398	IMR90	lung:	n/a	chr1:153583503-153583514 chr1:153584946-153584956 chr1:153583503-153583514 chr1:153583499-153583518 chr1:153583504-153583513 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583512 chr1:153583503-153583514 chr1:153585185-153585195 chr1:153583502-153583515 chr1:153584570-153584580 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583514 chr1:153586089-153586098
5	POLR2A	chr1:153585345-153585645	A549	lung:	n/a	n/a
6	TCF12	chr1:153585256-153585789	ECC-1	luminal epithelium:	n/a	n/a
7	E2F4	chr1:153585437-153585637	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:153584432-153586236	MCF-7	breast:	n/a	n/a
9	YY1	chr1:153585458-153585788	HCT-116	colon:	n/a	n/a
10	POLR2A	chr1:153585253-153585735	HUVEC	blood vessel:	n/a	n/a
11	SP1	chr1:153584935-153585868	A549	lung:	n/a	chr1:153585229-153585243 chr1:153585669-153585683 chr1:153584946-153584958 chr1:153584946-153584958 chr1:153584948-153584957 chr1:153585229-153585238
12	CTBP2	chr1:153585398-153586207	H1-hESC	embryonic stem cell:	n/a	n/a
13	TCF12	chr1:153585090-153586007	ECC-1	luminal epithelium:	n/a	chr1:153585856-153585864
14	GTF2F1	chr1:153585403-153586060	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:153585129-153585672	HepG2	liver:	n/a	n/a
16	SIN3A	chr1:153585482-153585701	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr1:153585238-153586329	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr1:153585041-153585738	U87	brain:	n/a	n/a
19	REST	chr1:153585222-153585698	A549	lung:	n/a	n/a
20	HEY1	chr1:153585319-153585594	HepG2	liver:	n/a	n/a
21	FOXA1	chr1:153585395-153585700	T-47D	breast:	n/a	n/a
22	SIN3AK20	chr1:153585373-153585616	A549	lung:	n/a	n/a
23	TAF1	chr1:153585333-153585655	Hela-S3	cervix:	n/a	n/a
24	MAX	chr1:153585389-153585745	Hela-S3	cervix:	n/a	n/a
25	MAX	chr1:153585281-153585910	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr1:153584990-153585633	HepG2	liver:	n/a	n/a
27	ZNF143	chr1:153585412-153585644	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr1:153584925-153585719	HepG2	liver:	n/a	n/a
29	FOXA1	chr1:153585377-153585731	T-47D	breast:	n/a	n/a
30	FOS	chr1:153585556-153585794	MCF10A-Er-Src	breast:	n/a	n/a
31	NFIC	chr1:153585354-153585889	ECC-1	luminal epithelium:	n/a	n/a
32	ELK1	chr1:153585423-153585671	Hela-S3	cervix:	n/a	n/a
33	ZKSCAN1	chr1:153585417-153586265	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr1:153585321-153585636	A549	lung:	n/a	n/a
35	CEBPB	chr1:153585455-153585697	Hela-S3	cervix:	n/a	n/a
36	RAD21	chr1:153585479-153585685	Hela-S3	cervix:	n/a	n/a
37	TCF7L2	chr1:153585430-153585664	Hela-S3	cervix:	n/a	n/a
38	GATA3	chr1:153585351-153585794	T-47D	breast:	n/a	n/a
39	ZBTB7A	chr1:153584706-153585836	ECC-1	luminal epithelium:	n/a	n/a
40	CHD2	chr1:153585395-153585935	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr1:153585366-153585844	Hela-S3	cervix:	n/a	n/a
42	MAFK	chr1:153585433-153585807	Hela-S3	cervix:	n/a	n/a
43	MAZ	chr1:153585448-153585734	K562	blood:	n/a	n/a
44	MAZ	chr1:153584585-153586025	Hela-S3	cervix:	n/a	chr1:153584946-153584956 chr1:153585185-153585195
45	HEY1	chr1:153584918-153585619	HepG2	liver:	n/a	n/a
46	TAF1	chr1:153585147-153585768	A549	lung:	n/a	n/a
47	POLR2A	chr1:153585184-153586050	Hela-S3	cervix:	n/a	n/a
48	SP1	chr1:153585082-153585591	HepG2	liver:	n/a	chr1:153585229-153585243 chr1:153585229-153585238
49	POLR2A	chr1:153585278-153585724	Hela-S3	cervix:	n/a	n/a
50	RAD21	chr1:153585555-153585608	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153580618..153585586-chr1:153936399..153942199,7	MCF-7	breast:
2	chr1:153505889..153508485-chr1:153582874..153585873,3	MCF-7	breast:
3	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
4	chr1:153519212..153523090-chr1:153584863..153588698,4	MCF-7	breast:
5	chr1:153584270..153586809-chr1:153629991..153631660,2	MCF-7	breast:
6	chr1:153585070..153587943-chr1:153641105..153643486,2	MCF-7	breast:
7	chr1:153585260..153586066-chr19:58987248..58987941,2	HCT-116	colon:
8	chr1:153536449..153542914-chr1:153579157..153590800,34	MCF-7	breast:
9	chr1:153505490..153510008-chr1:153584041..153589482,7	MCF-7	breast:

Variant related genes	Relation type
S100A16	TF binding region
ENSG00000273026	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000083838	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000143553	Chromatin interaction
ENSG00000188015	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1046381	0.80[ASN][1000 genomes]
rs10797096	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs11265625	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs11497739	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11548102	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11548103	0.94[ASN][1000 genomes]
rs11548104	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs28416529	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs28754733	0.92[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[ASN][1000 genomes]
rs35760493	0.94[ASN][1000 genomes]
rs35890901	0.84[ASN][1000 genomes]
rs3806233	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3862047	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs4072425	0.89[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4515830	0.83[CEU][hapmap]
rs4845563	0.80[CEU][hapmap];0.84[TSI][hapmap]
rs6674929	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs9330298	0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9330299	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9330300	0.92[ASN][1000 genomes]
rs9330301	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9660679	0.94[ASN][1000 genomes]
rs9662664	0.82[TSI][hapmap]
rs9699949	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9700928	0.84[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9726753	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9729773	0.92[ASN][1000 genomes]
rs9792913	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9792963	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9792967	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9793310	0.94[ASN][1000 genomes]
rs999418	0.92[ASN][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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs9700179	CTSS	cis	parietal	SCAN
rs9700179	FLG	cis	cerebellum	SCAN
rs9700179	S100A2	cis	cerebellum	SCAN
rs9700179	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs9700179	LCE2D	cis	cerebellum	SCAN
rs9700179	GATAD2B	cis	cerebellum	SCAN
rs9700179	S100A13	cis	parietal	SCAN
rs9700179	S100A10	cis	cerebellum	SCAN
rs9700179	S100A13	cis	lymphoblastoid	seeQTL
rs9700179	S100A16	cis	cerebellum	SCAN
rs9700179	ZNF687	cis	cerebellum	SCAN
rs9700179	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs9700179	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs9700179	S100A16	cis	parietal	SCAN
rs9700179	S100A14	cis	Esophagus Mucosa	GTEx
rs9700179	SLC27A3	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153582800-153585600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:153582800-153591200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:153583000-153589000	Active TSS	Esophagus	oesophagus
4	chr1:153583200-153585600	Active TSS	Muscle Satellite Cultured Cells	--
5	chr1:153583200-153585600	Active TSS	HSMM	muscle
6	chr1:153583200-153585800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:153583200-153585800	Active TSS	HMEC	breast
8	chr1:153583200-153585800	Active TSS	NHLF	lung
9	chr1:153583200-153586000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:153583600-153585600	Active TSS	Sigmoid Colon	Sigmoid Colon
11	chr1:153583600-153585800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:153583600-153585800	Active TSS	A549	lung
13	chr1:153583600-153590000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:153583800-153585600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:153583800-153585600	Active TSS	Brain Hippocampus Middle	brain
16	chr1:153583800-153586200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:153584000-153585600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:153584000-153585600	Active TSS	Brain Anterior Caudate	brain
19	chr1:153584000-153585600	Active TSS	Brain Cingulate Gyrus	brain
20	chr1:153584000-153585800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:153584000-153585800	Active TSS	Ovary	ovary
22	chr1:153584000-153585800	Active TSS	NHDF-Ad	bronchial
23	chr1:153584000-153588600	Weak transcription	K562	blood
24	chr1:153584200-153585600	Active TSS	Aorta	Aorta
25	chr1:153584200-153585600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:153584200-153585600	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr1:153584200-153585600	Active TSS	Gastric	stomach
28	chr1:153584200-153585600	Active TSS	Lung	lung
29	chr1:153584200-153585600	Active TSS	Small Intestine	intestine
30	chr1:153584200-153585600	Active TSS	HSMMtube	muscle
31	chr1:153584200-153585600	Active TSS	HUVEC	blood vessel
32	chr1:153584200-153585800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:153584200-153585800	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr1:153584200-153585800	Enhancers	Fetal Brain Male	brain
35	chr1:153584200-153585800	Flanking Active TSS	Fetal Muscle Trunk	muscle
36	chr1:153584200-153585800	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr1:153584200-153585800	Active TSS	Psoas Muscle	Psoas
38	chr1:153584200-153585800	Active TSS	NH-A	brain
39	chr1:153584200-153586000	Active TSS	Duodenum Mucosa	Duodenum
40	chr1:153584200-153588600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr1:153584200-153588800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr1:153584400-153585600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:153584400-153585600	Active TSS	Fetal Intestine Small	intestine
44	chr1:153584400-153585600	Active TSS	Stomach Mucosa	stomach
45	chr1:153584400-153585600	Active TSS	Hela-S3	cervix
46	chr1:153584400-153585600	Active TSS	Osteobl	bone
47	chr1:153584400-153585800	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr1:153584400-153585800	Active TSS	Colon Smooth Muscle	Colon
49	chr1:153584400-153585800	Active TSS	Fetal Kidney	kidney
50	chr1:153584400-153585800	Active TSS	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links