Variant report

Variant	rs34772253
Chromosome Location	chr1:153939495-153939496
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	STAT5A	chr1:153939401-153940729	GM12878	blood:	n/a	n/a
2	FOSL2	chr1:153939376-153940605	A549	lung:	n/a	n/a
3	POLR2A	chr1:153939452-153940652	K562	blood:	n/a	n/a
4	POLR2A	chr1:153939484-153940667	GM12892	blood:	n/a	n/a
5	TAF1	chr1:153939493-153941042	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:153938950-153940700	GM12878	blood:	n/a	n/a
7	RFX5	chr1:153939417-153939878	K562	blood:	n/a	n/a
8	POLR2A	chr1:153939399-153940861	PFSK-1	brain:	n/a	n/a
9	MAX	chr1:153939423-153940622	SK-N-SH	brain:	n/a	chr1:153939838-153939847 chr1:153939837-153939848 chr1:153939838-153939847 chr1:153939833-153939852 chr1:153939836-153939849
10	USF1	chr1:153939401-153940777	HCT-116	colon:	n/a	n/a
11	MAFK	chr1:153939492-153939847	H1-hESC	embryonic stem cell:	n/a	n/a
12	RFX5	chr1:153939044-153940690	Hela-S3	cervix:	n/a	n/a
13	CREB1	chr1:153939437-153940591	GM12878	blood:	n/a	n/a
14	MAX	chr1:153939071-153940597	Hela-S3	cervix:	n/a	chr1:153939838-153939847 chr1:153939837-153939848 chr1:153939838-153939847 chr1:153939833-153939852 chr1:153939836-153939849
15	SP1	chr1:153939329-153940713	HCT-116	colon:	n/a	chr1:153940670-153940679 chr1:153940670-153940679 chr1:153940669-153940678 chr1:153940665-153940679 chr1:153940668-153940680 chr1:153940668-153940680 chr1:153940669-153940679 chr1:153940669-153940679
16	TBL1XR1	chr1:153939295-153940755	K562	blood:	n/a	n/a
17	HCFC1	chr1:153939385-153940547	K562	blood:	n/a	n/a
18	BCL3	chr1:153939436-153940514	A549	lung:	n/a	chr1:153939732-153939741
19	REST	chr1:153939343-153940726	A549	lung:	n/a	n/a
20	E2F4	chr1:153939452-153940723	MCF10A-Er-Src	breast:	n/a	chr1:153939845-153939856 chr1:153940669-153940678
21	ETS1	chr1:153939446-153939813	A549	lung:	n/a	n/a
22	POLR2A	chr1:153939407-153940649	GM12878	blood:	n/a	n/a
23	TAF1	chr1:153939493-153940596	K562	blood:	n/a	n/a
24	MAX	chr1:153939390-153940758	HepG2	liver:	n/a	chr1:153939838-153939847 chr1:153939837-153939848 chr1:153939838-153939847 chr1:153939833-153939852 chr1:153939836-153939849
25	MAX	chr1:153939304-153941038	HCT-116	colon:	n/a	chr1:153939838-153939847 chr1:153939837-153939848 chr1:153939838-153939847 chr1:153939833-153939852 chr1:153939836-153939849
26	STAT1	chr1:153939450-153940540	GM12878	blood:	n/a	chr1:153939875-153939886
27	JUN	chr1:153938999-153941490	K562	blood:	n/a	chr1:153940887-153940896 chr1:153940888-153940897
28	NFIC	chr1:153939313-153940033	GM12878	blood:	n/a	n/a
29	SIN3AK20	chr1:153939018-153941202	MCF-7	breast:	n/a	n/a
30	TBP	chr1:153939170-153940597	GM12878	blood:	n/a	n/a
31	FOXM1	chr1:153939436-153940567	GM12878	blood:	n/a	n/a
32	POLR2A	chr1:153939460-153940673	GM19099	blood:	n/a	n/a
33	MYC	chr1:153939454-153940569	K562	blood:	n/a	chr1:153939838-153939847 chr1:153939837-153939848 chr1:153939838-153939847 chr1:153939833-153939852 chr1:153939836-153939849
34	KAP1	chr1:153939098-153940614	U2OS	brain:	n/a	n/a
35	MYC	chr1:153939235-153941336	K562	blood:	n/a	chr1:153939838-153939847 chr1:153939837-153939848 chr1:153939838-153939847 chr1:153939833-153939852 chr1:153939836-153939849
36	POU2F2	chr1:153939446-153940547	GM12878	blood:	n/a	n/a
37	NR2F2	chr1:153939484-153940780	K562	blood:	n/a	n/a
38	NFIC	chr1:153939063-153940549	GM12878	blood:	n/a	n/a
39	GABPA	chr1:153939464-153940680	SK-N-SH	brain:	n/a	chr1:153940669-153940678
40	TAF1	chr1:153939410-153940279	ECC-1	luminal epithelium:	n/a	n/a
41	MYC	chr1:153939115-153941357	K562	blood:	n/a	chr1:153939838-153939847 chr1:153939837-153939848 chr1:153939838-153939847 chr1:153939833-153939852 chr1:153939836-153939849
42	POLR2A	chr1:153939418-153940629	GM12891	blood:	n/a	n/a
43	BRCA1	chr1:153939163-153940587	Hela-S3	cervix:	n/a	n/a
44	USF1	chr1:153939468-153940484	A549	lung:	n/a	n/a
45	POLR2A	chr1:153939091-153940597	K562	blood:	n/a	n/a
46	TCF12	chr1:153939235-153940706	A549	lung:	n/a	n/a
47	MAFK	chr1:153939097-153940704	Hela-S3	cervix:	n/a	n/a
48	JUND	chr1:153939226-153940440	H1-hESC	embryonic stem cell:	n/a	n/a
49	SP1	chr1:153939319-153940932	HCT-116	colon:	n/a	chr1:153940670-153940679 chr1:153940888-153940900 chr1:153940670-153940679 chr1:153940889-153940898 chr1:153940669-153940678 chr1:153940885-153940899 chr1:153940665-153940679 chr1:153940668-153940680 chr1:153940890-153940899 chr1:153940668-153940680 chr1:153940888-153940900 chr1:153940669-153940679 chr1:153940669-153940679 chr1:153940890-153940899
50	USF1	chr1:153939404-153940146	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153936330..153941464-chr1:154191669..154195552,8	MCF-7	breast:
2	chr1:153605540..153608540-chr1:153937612..153940414,3	MCF-7	breast:
3	chr1:153939275..153939790-chr7:100026970..100027477,2	Hela-S3	cervix:
4	chr1:153938901..153941053-chr16:89004507..89006484,2	MCF-7	breast:
5	chr1:149857983..149858591-chr1:153939337..153940220,2	Hela-S3	cervix:
6	chr1:153939459..153939974-chr1:169862891..169863399,2	Hela-S3	cervix:
7	chr1:153641625..153644878-chr1:153937648..153941391,3	K562	blood:
8	chr1:153742918..153749628-chr1:153933334..153942122,16	MCF-7	breast:
9	chr1:153580618..153585586-chr1:153936399..153942199,7	MCF-7	breast:
10	chr1:153603827..153606641-chr1:153939224..153941084,2	MCF-7	breast:
11	chr1:153640832..153646304-chr1:153937039..153940655,5	MCF-7	breast:
12	chr1:153938202..153942686-chr1:154154566..154158952,5	MCF-7	breast:
13	chr1:153599605..153601359-chr1:153938449..153940087,2	MCF-7	breast:
14	chr1:153747310..153750060-chr1:153937716..153939765,3	MCF-7	breast:
15	chr1:153939104..153942755-chr1:154191760..154194945,4	MCF-7	breast:
16	chr1:153939426..153939978-chr6:36562838..36563356,2	Hela-S3	cervix:
17	chr1:153939194..153941936-chr6:27857839..27860043,2	MCF-7	breast:
18	chr1:153938923..153939839-chr3:38206200..38207525,3	NB4	blood:

Variant related genes	Relation type
SLC39A1	TF binding region
CREB3L4	TF binding region
ENSG00000184678	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000172939	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000000457	Chromatin interaction
ENSG00000205018	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000261226	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000143569	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11265027	1.00[LWK][hapmap]
rs12755932	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
6	nsv532552	chr1:153912047-153950752	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers 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 miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153936800-153939600	Weak transcription	Gastric	stomach
2	chr1:153936800-153939600	Weak transcription	Small Intestine	intestine
3	chr1:153937000-153939600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:153937000-153939600	Weak transcription	Esophagus	oesophagus
5	chr1:153937400-153939600	Weak transcription	Lung	lung
6	chr1:153938400-153939600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr1:153938400-153939600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr1:153938400-153939600	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr1:153938400-153939600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr1:153938400-153939800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:153938400-153940000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:153938400-153941000	Active TSS	A549	lung
13	chr1:153938400-153941400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr1:153938600-153939600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr1:153938600-153939600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:153938600-153939800	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr1:153938600-153939800	Flanking Active TSS	HUVEC	blood vessel
18	chr1:153938600-153941200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:153938800-153939600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:153938800-153939600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:153938800-153940400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:153938800-153940400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:153938800-153940400	Active TSS	HSMM	muscle
24	chr1:153938800-153940600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:153938800-153940600	Active TSS	Fetal Intestine Small	intestine
26	chr1:153938800-153940600	Active TSS	GM12878-XiMat	blood
27	chr1:153938800-153940800	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr1:153938800-153941000	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr1:153938800-153941000	Active TSS	Fetal Brain Female	brain
30	chr1:153938800-153941200	Active TSS	K562	blood
31	chr1:153938800-153941400	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr1:153938800-153941600	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr1:153939000-153939600	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr1:153939000-153939600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:153939000-153939600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr1:153939000-153939600	Flanking Active TSS	Liver	Liver
37	chr1:153939000-153939600	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr1:153939000-153939600	Flanking Active TSS	Fetal Heart	heart
39	chr1:153939000-153939600	Weak transcription	Pancreas	Pancrea
40	chr1:153939000-153939600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr1:153939000-153939600	Weak transcription	Spleen	Spleen
42	chr1:153939000-153939600	Flanking Active TSS	NHLF	lung
43	chr1:153939000-153939800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr1:153939000-153939800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr1:153939000-153939800	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr1:153939000-153940000	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr1:153939000-153940000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr1:153939000-153940400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:153939000-153940400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:153939000-153940800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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