Variant report

Variant	rs2438709
Chromosome Location	chr2:97199694-97199695
allele	C/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	RCOR1	chr2:97199586-97199890	K562	blood:	n/a	n/a
2	POLR2A	chr2:97199056-97199787	HL-60	blood:	n/a	n/a
3	STAT3	chr2:97199270-97199758	MCF10A-Er-Src	breast:	n/a	chr2:97199281-97199289
4	MAZ	chr2:97199091-97199711	Hela-S3	cervix:	n/a	n/a
5	TFAP2C	chr2:97198885-97199914	Hela-S3	cervix:	n/a	n/a
6	RFX5	chr2:97199317-97199794	Hela-S3	cervix:	n/a	chr2:97199611-97199619
7	ZNF143	chr2:97199620-97199814	K562	blood:	n/a	n/a
8	EP300	chr2:97199588-97201132	SK-N-SH	brain:	n/a	n/a
9	TCF7L2	chr2:97199216-97199855	Hela-S3	cervix:	n/a	chr2:97199579-97199586
10	RCOR1	chr2:97199493-97199878	Hela-S3	cervix:	n/a	n/a
11	ZNF143	chr2:97199674-97199787	GM12878	blood:	n/a	n/a
12	EBF1	chr2:97198802-97199831	GM12878	blood:	n/a	chr2:97199024-97199034 chr2:97199024-97199033 chr2:97199021-97199032
13	FOS	chr2:97199369-97199768	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr2:97198966-97199754	HL-60	blood:	n/a	n/a
15	MAX	chr2:97199109-97199699	Hela-S3	cervix:	n/a	n/a
16	FOS	chr2:97199353-97199767	MCF10A-Er-Src	breast:	n/a	n/a
17	CEBPB	chr2:97199331-97199745	Hela-S3	cervix:	n/a	n/a
18	MYC	chr2:97199205-97199846	MCF10A-Er-Src	breast:	n/a	n/a
19	GATA3	chr2:97199409-97199720	T-47D	breast:	n/a	n/a
20	SPI1	chr2:97199032-97199817	HL-60	blood:	n/a	n/a
21	TCF7L2	chr2:97199385-97200846	PANC-1	pancreas:	n/a	chr2:97199579-97199586
22	MYC	chr2:97199306-97199931	MCF10A-Er-Src	breast:	n/a	n/a
23	ZNF143	chr2:97199506-97199863	Hela-S3	cervix:	n/a	n/a
24	TFAP2A	chr2:97199138-97199925	Hela-S3	cervix:	n/a	chr2:97199664-97199679
25	KAP1	chr2:97199347-97200334	U2OS	brain:	n/a	n/a
26	STAT3	chr2:97199297-97199697	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr2:97199283-97199699	MCF10A-Er-Src	breast:	n/a	n/a
28	STAT3	chr2:97199247-97199817	MCF10A-Er-Src	breast:	n/a	chr2:97199281-97199289
29	RCOR1	chr2:97199564-97199917	K562	blood:	n/a	n/a

Variant related genes	Relation type
ARID5A	TF binding region
ENSG00000235480	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12477963	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap]
rs34029026	1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs772160	1.00[CHD][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3460902	chr2:97138421-97459342	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	esv3460903	chr2:97138421-97459342	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv999871	chr2:97157196-97407711	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv535829	chr2:97157196-97407711	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97193200-97201000	Enhancers	NHDF-Ad	bronchial
2	chr2:97194000-97202600	Enhancers	Placenta	Placenta
3	chr2:97194400-97202400	Enhancers	Lung	lung
4	chr2:97194800-97202000	Weak transcription	Liver	Liver
5	chr2:97196200-97200800	Enhancers	NHLF	lung
6	chr2:97197000-97201800	Enhancers	HSMMtube	muscle
7	chr2:97197200-97199800	Enhancers	Spleen	Spleen
8	chr2:97197200-97200400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr2:97197200-97200600	Enhancers	Fetal Lung	lung
10	chr2:97197200-97200600	Enhancers	Stomach Mucosa	stomach
11	chr2:97197200-97202400	Enhancers	Brain Angular Gyrus	brain
12	chr2:97197200-97202400	Enhancers	Gastric	stomach
13	chr2:97197400-97200000	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr2:97197400-97200000	Enhancers	A549	lung
15	chr2:97197400-97202400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:97197400-97202400	Enhancers	Psoas Muscle	Psoas
17	chr2:97197600-97199800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:97197800-97200400	Enhancers	Osteobl	bone
19	chr2:97197800-97200600	Enhancers	Primary hematopoietic stem cells	blood
20	chr2:97197800-97202000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr2:97197800-97202400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr2:97198000-97199800	Enhancers	Primary B cells from peripheral blood	blood
23	chr2:97198000-97199800	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr2:97198000-97199800	Enhancers	Fetal Heart	heart
25	chr2:97198000-97199800	Enhancers	Fetal Thymus	thymus
26	chr2:97198000-97200000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:97198000-97200000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr2:97198000-97200200	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr2:97198000-97200600	Enhancers	Right Atrium	heart
30	chr2:97198000-97200800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:97198000-97200800	Enhancers	Brain Cingulate Gyrus	brain
32	chr2:97198000-97201000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:97198000-97201000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr2:97198000-97201000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:97198000-97201000	Enhancers	Brain Hippocampus Middle	brain
36	chr2:97198000-97201000	Enhancers	Fetal Stomach	stomach
37	chr2:97198000-97201200	Enhancers	Fetal Muscle Trunk	muscle
38	chr2:97198000-97202000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:97198000-97202000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:97198000-97202000	Enhancers	Adipose Nuclei	Adipose
41	chr2:97198000-97202000	Enhancers	Colonic Mucosa	Colon
42	chr2:97198000-97202000	Enhancers	Duodenum Mucosa	Duodenum
43	chr2:97198000-97202200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:97198000-97202200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:97198000-97202200	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr2:97198000-97202400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:97198000-97202400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:97198000-97202400	Enhancers	Left Ventricle	heart
49	chr2:97198000-97202400	Enhancers	Right Ventricle	heart
50	chr2:97198000-97202400	Enhancers	HMEC	breast

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