Variant report

Variant	rs28384429
Chromosome Location	chr17:33914131-33914132
allele	A/T
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	chr17:33913921-33914615	SK-N-MC	brain:	n/a	n/a
2	TCF12	chr17:33913990-33914566	A549	lung:	n/a	n/a
3	CREB1	chr17:33913762-33914696	A549	lung:	n/a	chr17:33914252-33914265
4	MYC	chr17:33913871-33915054	K562	blood:	n/a	chr17:33914048-33914057
5	ATF3	chr17:33913903-33914729	A549	lung:	n/a	chr17:33914275-33914285 chr17:33914251-33914264 chr17:33914251-33914262 chr17:33914278-33914288 chr17:33914252-33914262 chr17:33914251-33914266 chr17:33914255-33914262 chr17:33914277-33914288 chr17:33914278-33914288 chr17:33914253-33914264 chr17:33914252-33914265 chr17:33914278-33914285 chr17:33914275-33914286 chr17:33914254-33914262 chr17:33914253-33914264 chr17:33914243-33914263 chr17:33914252-33914265 chr17:33914255-33914263 chr17:33914274-33914289 chr17:33914252-33914263 chr17:33914275-33914285 chr17:33914252-33914262
6	CHD2	chr17:33914056-33914650	GM12878	blood:	n/a	n/a
7	POLR2A	chr17:33913952-33914972	K562	blood:	n/a	n/a
8	POLR2A	chr17:33913732-33915042	GM12892	blood:	n/a	n/a
9	STAT1	chr17:33914115-33914668	GM12878	blood:	n/a	n/a
10	POLR2A	chr17:33913740-33914931	K562	blood:	n/a	n/a
11	POU2F2	chr17:33914068-33914340	GM12878	blood:	n/a	n/a
12	POLR2A	chr17:33913822-33915080	K562	blood:	n/a	n/a
13	POLR2A	chr17:33913735-33914785	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr17:33913768-33914768	HUVEC	blood vessel:	n/a	n/a
15	MAX	chr17:33914086-33914730	H1-hESC	embryonic stem cell:	n/a	n/a
16	CEBPD	chr17:33914046-33914561	HepG2	liver:	n/a	n/a
17	SMC3	chr17:33913719-33914900	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr17:33913797-33914969	HepG2	liver:	n/a	n/a
19	YY1	chr17:33914110-33914482	K562	blood:	n/a	chr17:33914296-33914318
20	ATF2	chr17:33913959-33914746	GM12878	blood:	n/a	chr17:33914251-33914265
21	REST	chr17:33914095-33914558	PANC-1	pancreas:	n/a	n/a
22	CHD1	chr17:33913989-33914792	GM12878	blood:	n/a	n/a
23	ELK1	chr17:33914026-33914714	K562	blood:	n/a	n/a
24	YY1	chr17:33914064-33914514	GM12878	blood:	n/a	chr17:33914296-33914318
25	ETS1	chr17:33913995-33914583	GM12878	blood:	n/a	chr17:33914536-33914547 chr17:33914364-33914377
26	NRF1	chr17:33913981-33914544	GM12878	blood:	n/a	n/a
27	SP4	chr17:33914008-33914559	H1-hESC	embryonic stem cell:	n/a	n/a
28	ELF1	chr17:33914040-33914519	A549	lung:	n/a	n/a
29	YY1	chr17:33914084-33915050	K562	blood:	n/a	chr17:33914538-33914547 chr17:33914296-33914318
30	EGR1	chr17:33914012-33914783	HCT-116	colon:	n/a	chr17:33914405-33914419
31	FOSL2	chr17:33914038-33914538	A549	lung:	n/a	chr17:33914254-33914263 chr17:33914277-33914286
32	JUND	chr17:33914048-33915156	GM12878	blood:	n/a	chr17:33914254-33914263 chr17:33914277-33914286
33	ATF3	chr17:33913981-33914403	HepG2	liver:	n/a	chr17:33914275-33914285 chr17:33914251-33914264 chr17:33914251-33914262 chr17:33914278-33914288 chr17:33914252-33914262 chr17:33914251-33914266 chr17:33914255-33914262 chr17:33914277-33914288 chr17:33914278-33914288 chr17:33914253-33914264 chr17:33914252-33914265 chr17:33914278-33914285 chr17:33914275-33914286 chr17:33914254-33914262 chr17:33914253-33914264 chr17:33914243-33914263 chr17:33914252-33914265 chr17:33914255-33914263 chr17:33914274-33914289 chr17:33914252-33914263 chr17:33914275-33914285 chr17:33914252-33914262
34	FOS	chr17:33914130-33914518	MCF10A-Er-Src	breast:	n/a	chr17:33914254-33914263 chr17:33914277-33914286
35	ELF1	chr17:33914110-33914927	GM12878	blood:	n/a	chr17:33914538-33914547
36	GABPA	chr17:33913945-33914803	SK-N-SH	brain:	n/a	n/a
37	FOXM1	chr17:33914025-33914552	GM12878	blood:	n/a	n/a
38	BCLAF1	chr17:33914018-33914707	GM12878	blood:	n/a	n/a
39	SIN3AK20	chr17:33914048-33914893	K562	blood:	n/a	n/a
40	POLR2A	chr17:33913738-33914668	HCT-116	colon:	n/a	n/a
41	MAX	chr17:33914038-33915065	ECC-1	luminal epithelium:	n/a	chr17:33914048-33914057
42	TCF7L2	chr17:33914038-33914365	Hela-S3	cervix:	n/a	n/a
43	CHD2	chr17:33914032-33914826	K562	blood:	n/a	n/a
44	PAX5	chr17:33914014-33914672	GM12891	blood:	n/a	n/a
45	E2F4	chr17:33914121-33914575	MCF10A-Er-Src	breast:	n/a	chr17:33914278-33914287 chr17:33914276-33914285 chr17:33914255-33914264 chr17:33914253-33914262
46	JUN	chr17:33914083-33914463	HUVEC	blood vessel:	n/a	chr17:33914254-33914263 chr17:33914277-33914286 chr17:33914250-33914263
47	TAF1	chr17:33913925-33914753	PFSK-1	brain:	n/a	n/a
48	MEF2A	chr17:33913973-33914552	GM12878	blood:	n/a	n/a
49	TAF1	chr17:33914062-33914478	GM12891	blood:	n/a	n/a
50	TBL1XR1	chr17:33913968-33914521	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:33894766..33896836-chr17:33913022..33916399,3	MCF-7	breast:
2	chr17:33913527..33915363-chr17:34134013..34136643,3	MCF-7	breast:
3	chr17:33903370..33909494-chr17:33910892..33920548,27	MCF-7	breast:
4	chr17:33914064..33915012-chr6:26157639..26158403,2	Hela-S3	cervix:
5	chr17:33905180..33906102-chr17:33913821..33914729,3	K562	blood:
6	chr17:33914034..33914731-chr9:140506382..140507316,2	HCT-116	colon:
7	chr17:33913805..33914612-chr17:56708718..56709372,2	Hela-S3	cervix:
8	chr17:33913630..33915202-chr17:34134873..34137603,2	K562	blood:
9	chr17:33865496..33867936-chr17:33913565..33917669,3	K562	blood:
10	chr15:90931103..90932010-chr17:33913689..33914304,2	Hela-S3	cervix:
11	chr17:33913686..33914581-chr7:45039628..45040231,2	Hela-S3	cervix:
12	chr17:33913978..33914844-chrX:67718459..67719108,2	Hela-S3	cervix:
13	chr17:33905316..33906150-chr17:33913826..33914517,2	MCF-7	breast:

Variant related genes	Relation type
AP2B1	TF binding region
ENSG00000197070	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000267321	Chromatin interaction
ENSG00000172660	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000006125	Chromatin interaction
ENSG00000267035	Chromatin interaction
ENSG00000108733	Chromatin interaction
ENSG00000140575	Chromatin interaction
ENSG00000267578	Chromatin interaction
ENSG00000181704	Chromatin interaction
ENSG00000136280	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1037591	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10491114	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10491115	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11870399	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870475	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12449919	0.92[ASN][1000 genomes]
rs12450039	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12452633	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12452961	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12600662	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12603142	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16971117	0.85[AMR][1000 genomes]
rs16971122	0.85[AMR][1000 genomes]
rs1964509	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2079924	1.00[AFR][1000 genomes]
rs226433	0.92[ASN][1000 genomes]
rs226435	0.92[ASN][1000 genomes]
rs226436	0.92[ASN][1000 genomes]
rs226437	0.92[ASN][1000 genomes]
rs2278950	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2301731	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2428463	0.92[ASN][1000 genomes]
rs2523115	0.92[ASN][1000 genomes]
rs28384428	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661650	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3760325	1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3785759	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3785763	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs62079728	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7211363	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9303689	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9891317	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9904957	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9906037	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9914730	0.97[ASN][1000 genomes]
rs9916483	0.92[ASN][1000 genomes]

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	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1060890	chr17:33884124-34011034	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv543318	chr17:33884124-34011034	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33913600-33914200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
2	chr17:33913600-33914200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:33913600-33914200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr17:33913600-33914200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr17:33913600-33914200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr17:33913600-33914200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr17:33913600-33914200	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr17:33913600-33914200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr17:33913600-33914600	Active TSS	Primary B cells from cord blood	blood
10	chr17:33913600-33914800	Active TSS	Adipose Nuclei	Adipose
11	chr17:33913600-33915400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:33913600-33915400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr17:33913600-33915400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr17:33913600-33915400	Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr17:33913600-33915400	Active TSS	Brain Cingulate Gyrus	brain
16	chr17:33913600-33915400	Active TSS	Brain Hippocampus Middle	brain
17	chr17:33913600-33915400	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr17:33913600-33915400	Active TSS	Fetal Lung	lung
19	chr17:33913600-33915400	Active TSS	Rectal Smooth Muscle	rectum
20	chr17:33913600-33915400	Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr17:33913600-33915400	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr17:33913600-33915600	Active TSS	H1 Cell Line	embryonic stem cell
23	chr17:33913600-33915600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr17:33913600-33915600	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr17:33913600-33915600	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr17:33913600-33915600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr17:33913600-33915600	Active TSS	GM12878-XiMat	blood
28	chr17:33913600-33915800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr17:33913600-33915800	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr17:33913600-33916200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr17:33913600-33916400	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr17:33913600-33916400	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr17:33913600-33916400	Active TSS	HMEC	breast
34	chr17:33913600-33916800	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr17:33913800-33914200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr17:33913800-33914200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr17:33913800-33914200	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr17:33913800-33914200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr17:33913800-33914200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr17:33913800-33914200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr17:33913800-33914200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr17:33913800-33914200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr17:33913800-33914200	Flanking Active TSS	Fetal Brain Male	brain
44	chr17:33913800-33914200	Flanking Active TSS	Fetal Heart	heart
45	chr17:33913800-33914200	Flanking Active TSS	Fetal Stomach	stomach
46	chr17:33913800-33914200	Flanking Active TSS	Fetal Thymus	thymus
47	chr17:33913800-33914200	Flanking Active TSS	HepG2	liver
48	chr17:33913800-33914200	Flanking Active TSS	HUVEC	blood vessel
49	chr17:33913800-33914200	Flanking Active TSS	NHLF	lung
50	chr17:33913800-33914200	Flanking Active TSS	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links