Variant report

Variant	rs11892545
Chromosome Location	chr2:234338935-234338936
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	TAF1	chr2:234338883-234339166	SK-N-SH	brain:	n/a	n/a
2	CEBPB	chr2:234338587-234339225	A549	lung:	n/a	n/a
3	MYC	chr2:234338737-234339011	MCF10A-Er-Src	breast:	n/a	n/a
4	NFIC	chr2:234338472-234339310	SK-N-SH	brain:	n/a	n/a
5	SP1	chr2:234338580-234339253	A549	lung:	n/a	n/a
6	FOS	chr2:234338881-234339023	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr2:234338811-234339079	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr2:234338844-234339106	MCF10A-Er-Src	breast:	n/a	chr2:234338866-234338877
9	STAT3	chr2:234338754-234339033	MCF10A-Er-Src	breast:	n/a	chr2:234338866-234338877
10	GATA3	chr2:234338738-234339067	T-47D	breast:	n/a	n/a
11	SP1	chr2:234338562-234339261	A549	lung:	n/a	n/a
12	TEAD4	chr2:234338618-234339296	SK-N-SH	brain:	n/a	n/a
13	EP300	chr2:234338623-234339231	A549	lung:	n/a	n/a
14	USF2	chr2:234338887-234339050	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr2:234338813-234338965	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr2:234338659-234339150	SK-N-SH	brain:	n/a	n/a
17	TCF12	chr2:234338599-234339238	A549	lung:	n/a	n/a
18	POLR2A	chr2:234338646-234339097	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr2:234338763-234339023	MCF10A-Er-Src	breast:	n/a	n/a
20	PBX3	chr2:234338569-234339282	SK-N-SH	brain:	n/a	n/a
21	EP300	chr2:234338709-234339324	SK-N-SH	brain:	n/a	n/a
22	JUN	chr2:234338728-234339109	HUVEC	blood vessel:	n/a	n/a
23	GATA3	chr2:234338504-234339750	SK-N-SH	brain:	n/a	chr2:234339238-234339246 chr2:234339235-234339248
24	GATA3	chr2:234338479-234339718	SK-N-SH	brain:	n/a	chr2:234339238-234339246 chr2:234339235-234339248
25	FOSL2	chr2:234338604-234339216	A549	lung:	n/a	n/a
26	MAX	chr2:234338742-234339220	Hela-S3	cervix:	n/a	n/a
27	GATA3	chr2:234338695-234339236	SH-SY5Y	brain:	n/a	n/a
28	CEBPB	chr2:234338624-234339163	Hela-S3	cervix:	n/a	n/a
29	JUND	chr2:234338570-234339272	SK-N-SH	brain:	n/a	n/a
30	JUND	chr2:234338617-234339214	SK-N-SH	brain:	n/a	n/a
31	EP300	chr2:234338576-234339233	A549	lung:	n/a	n/a
32	PBX3	chr2:234338634-234339196	SK-N-SH	brain:	n/a	n/a
33	STAT3	chr2:234338749-234339037	Hela-S3	cervix:	n/a	chr2:234338866-234338877
34	FOSL2	chr2:234338574-234339276	SK-N-SH	brain:	n/a	n/a
35	GATA2	chr2:234338701-234339175	HUVEC	blood vessel:	n/a	n/a
36	GATA3	chr2:234338602-234339212	MCF-7	breast:	n/a	n/a
37	FOXA1	chr2:234338821-234339051	T-47D	breast:	n/a	n/a
38	MAX	chr2:234338712-234339134	SK-N-SH	brain:	n/a	n/a
39	EP300	chr2:234338516-234339298	SK-N-SH	brain:	n/a	n/a
40	FOSL2	chr2:234338758-234339062	A549	lung:	n/a	n/a
41	POLR2A	chr2:234338714-234339141	HUVEC	blood vessel:	n/a	n/a
42	TCF12	chr2:234338517-234339309	SK-N-SH	brain:	n/a	n/a
43	STAT3	chr2:234338742-234339050	MCF10A-Er-Src	breast:	n/a	chr2:234338866-234338877
44	ELF1	chr2:234338731-234339241	SK-N-SH	brain:	n/a	n/a
45	CEBPB	chr2:234338680-234339066	A549	lung:	n/a	n/a
46	E2F4	chr2:234338927-234339010	MCF10A-Er-Src	breast:	n/a	n/a
47	ELF1	chr2:234338627-234339374	SK-N-SH	brain:	n/a	n/a
48	TCF12	chr2:234338598-234339327	SK-N-SH	brain:	n/a	n/a
49	STAT3	chr2:234338719-234339050	MCF10A-Er-Src	breast:	n/a	chr2:234338866-234338877
50	GATA3	chr2:234338433-234339371	A549	lung:	n/a	chr2:234339238-234339246 chr2:234339235-234339248

No.	Distal block	Cell Line	Cell type
1	chr2:234337631..234339943-chr2:234342706..234345543,2	K562	blood:
2	chr2:234326124..234329247-chr2:234337323..234339781,4	MCF-7	breast:
3	chr2:234333282..234336244-chr2:234336565..234338970,2	K562	blood:
4	chr2:234331362..234333513-chr2:234338098..234340435,2	MCF-7	breast:
5	chr2:234326778..234329463-chr2:234337161..234339349,2	MCF-7	breast:

Variant related genes	Relation type
DGKD	TF binding region
ENSG00000077044	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10168794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs10177112	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10177761	0.83[EUR][1000 genomes]
rs10181039	0.93[EUR][1000 genomes]
rs10193542	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10199833	1.00[CHB][hapmap]
rs1037451	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10929208	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11888993	0.85[EUR][1000 genomes]
rs11895231	0.85[EUR][1000 genomes]
rs12467878	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13384932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13391864	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs13392183	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13400471	0.80[EUR][1000 genomes]
rs13400563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13403169	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs13414407	1.00[CEU][hapmap];0.94[GIH][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap];0.93[EUR][1000 genomes]
rs13419277	0.93[EUR][1000 genomes]
rs13425849	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs13427703	1.00[CHB][hapmap]
rs1542325	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1901812	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2124045	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2289473	1.00[CHB][hapmap]
rs2305541	0.86[AMR][1000 genomes]
rs28444082	0.93[EUR][1000 genomes]
rs28506837	0.93[EUR][1000 genomes]
rs28588417	0.88[EUR][1000 genomes]
rs2924809	1.00[JPT][hapmap]
rs2971865	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap]
rs3762591	0.93[EUR][1000 genomes]
rs3792104	1.00[CHB][hapmap]
rs3792105	1.00[CHB][hapmap]
rs4047198	1.00[JPT][hapmap]
rs4047199	1.00[JPT][hapmap]
rs4663698	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6713866	0.90[EUR][1000 genomes]
rs6716988	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6720619	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6726184	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6745134	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs73117507	0.93[EUR][1000 genomes]
rs73117551	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7422734	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap]
rs7572257	0.88[CEU][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs7588509	1.00[CHB][hapmap]
rs838557	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs838558	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs838561	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs838562	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv1000870	chr2:234333083-234410768	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234322400-234371800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:234328800-234343000	Weak transcription	Liver	Liver
3	chr2:234329000-234339200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr2:234329000-234343600	Weak transcription	Fetal Brain Female	brain
5	chr2:234329000-234351600	Weak transcription	Fetal Brain Male	brain
6	chr2:234329200-234343800	Weak transcription	Brain Germinal Matrix	brain
7	chr2:234329200-234344600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:234329400-234343200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:234329400-234343400	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:234329400-234344600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:234329400-234346000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:234330800-234343200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:234331000-234344000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:234331200-234340400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:234331200-234343400	Weak transcription	Thymus	Thymus
16	chr2:234331200-234344000	Weak transcription	Dnd41	blood
17	chr2:234331200-234344600	Weak transcription	Esophagus	oesophagus
18	chr2:234331600-234344400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:234332600-234339800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr2:234333200-234343200	Weak transcription	HepG2	liver
21	chr2:234333200-234344000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:234333400-234343000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:234333400-234343000	Weak transcription	Colonic Mucosa	Colon
24	chr2:234333400-234343000	Weak transcription	Spleen	Spleen
25	chr2:234333400-234344600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:234333400-234345600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:234333600-234339200	Enhancers	Stomach Mucosa	stomach
28	chr2:234333600-234343000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:234333600-234343200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr2:234333600-234343400	Weak transcription	Lung	lung
31	chr2:234333800-234343800	Weak transcription	Fetal Intestine Large	intestine
32	chr2:234334000-234343400	Weak transcription	Fetal Intestine Small	intestine
33	chr2:234334200-234339800	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr2:234334200-234340200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:234334400-234339400	Enhancers	HSMM	muscle
36	chr2:234334800-234339200	Enhancers	K562	blood
37	chr2:234335200-234357600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:234335400-234339800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr2:234335400-234340000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr2:234335600-234340400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:234335600-234343200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr2:234335600-234343600	Strong transcription	Primary B cells from cord blood	blood
43	chr2:234335600-234344000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:234335600-234344000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr2:234335600-234344800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:234335800-234339200	Enhancers	Primary T cells fromperipheralblood	blood
47	chr2:234335800-234344200	Weak transcription	Small Intestine	intestine
48	chr2:234336000-234343400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:234336000-234343400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:234336000-234343400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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