Variant report

Variant	rs2579505
Chromosome Location	chr2:97167962-97167963
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	ELF1	chr2:97167153-97168304	GM12878	blood:	n/a	n/a
2	MAZ	chr2:97167740-97168022	HepG2	liver:	n/a	n/a
3	MAX	chr2:97167830-97168130	HepG2	liver:	n/a	n/a
4	HNF4A	chr2:97167652-97168025	HepG2	liver:	n/a	chr2:97167865-97167887 chr2:97167809-97167821 chr2:97167834-97167846 chr2:97167808-97167822 chr2:97167868-97167883 chr2:97167809-97167821 chr2:97167891-97167899
5	MAX	chr2:97167509-97168377	HepG2	liver:	n/a	n/a
6	MXI1	chr2:97167675-97168111	HepG2	liver:	n/a	n/a
7	HEY1	chr2:97167665-97168121	HepG2	liver:	n/a	n/a
8	HNF4G	chr2:97167593-97168088	HepG2	liver:	n/a	chr2:97167865-97167887 chr2:97167869-97167884 chr2:97167809-97167821 chr2:97167834-97167846 chr2:97167806-97167821 chr2:97167808-97167822 chr2:97167809-97167821 chr2:97167891-97167899
9	HDAC2	chr2:97167691-97168041	HepG2	liver:	n/a	n/a
10	RFX5	chr2:97167434-97168195	HepG2	liver:	n/a	n/a
11	RCOR1	chr2:97167811-97168018	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:97167612-97168190	HepG2	liver:	n/a	n/a
13	POLR2A	chr2:97167725-97167966	HepG2	liver:	n/a	n/a
14	BHLHE40	chr2:97167633-97168212	HepG2	liver:	n/a	chr2:97168174-97168190
15	ZEB1	chr2:97167269-97168338	HepG2	liver:	n/a	n/a
16	RXRA	chr2:97167652-97167990	HepG2	liver:	n/a	chr2:97167834-97167848 chr2:97167807-97167823
17	STAT1	chr2:97167305-97168113	GM12878	blood:	n/a	chr2:97167325-97167332
18	POLR2A	chr2:97167548-97168254	HepG2	liver:	n/a	n/a
19	POLR2A	chr2:97167740-97168073	HepG2	liver:	n/a	n/a
20	MYC	chr2:97167950-97168082	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:97167695..97169619-chr2:97172123..97173788,2	K562	blood:
2	chr2:97078679..97080974-chr2:97167541..97169500,2	MCF-7	breast:
3	chr2:97159215..97162572-chr2:97166820..97170028,3	MCF-7	breast:
4	chr2:97167730..97170080-chr2:97181467..97183228,2	MCF-7	breast:
5	chr2:96872356..96874747-chr2:97166751..97169019,2	K562	blood:
6	chr2:97096508..97099065-chr2:97167456..97170345,2	K562	blood:

Variant related genes	Relation type
NEURL3	TF binding region
ENSG00000084090	Chromatin interaction
ENSG00000204685	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1011040	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10209780	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12329128	0.81[CEU][hapmap]
rs12717781	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12992413	0.84[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13019986	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13029764	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs17685664	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2314109	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2464914	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2579502	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2708976	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2708977	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2708978	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34029026	0.84[CEU][hapmap]
rs3731938	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs596069	0.88[CEU][hapmap]
rs6576972	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6753667	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs749027	0.88[CEU][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs772156	0.84[CEU][hapmap]
rs772173	0.84[CEU][hapmap]
rs772174	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97166000-97168400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
2	chr2:97166000-97168800	Enhancers	Spleen	Spleen
3	chr2:97166400-97168000	Enhancers	Colonic Mucosa	Colon
4	chr2:97166400-97169600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:97166400-97170400	Enhancers	Lung	lung
6	chr2:97166600-97168400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:97166600-97168400	Enhancers	Esophagus	oesophagus
8	chr2:97166600-97168600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:97166600-97168800	Enhancers	GM12878-XiMat	blood
10	chr2:97166600-97169800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr2:97166600-97170000	Weak transcription	Gastric	stomach
12	chr2:97167000-97168200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:97167000-97168400	Enhancers	Primary hematopoietic stem cells	blood
14	chr2:97167000-97168400	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr2:97167000-97168400	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr2:97167000-97169200	Bivalent Enhancer	Adipose Nuclei	Adipose
17	chr2:97167000-97169600	Enhancers	Primary B cells from peripheral blood	blood
18	chr2:97167200-97168000	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr2:97167200-97168000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:97167200-97168000	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr2:97167200-97168000	Bivalent Enhancer	Fetal Stomach	stomach
22	chr2:97167200-97168200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:97167200-97168200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr2:97167200-97168200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:97167200-97168200	Bivalent Enhancer	Fetal Muscle Leg	muscle
26	chr2:97167200-97168400	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr2:97167200-97168400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr2:97167200-97168400	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr2:97167200-97168400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr2:97167200-97168600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr2:97167200-97168600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:97167200-97168800	Bivalent Enhancer	Placenta	Placenta
33	chr2:97167200-97168800	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr2:97167200-97169200	Enhancers	Duodenum Mucosa	Duodenum
35	chr2:97167200-97169200	Bivalent Enhancer	Stomach Mucosa	stomach
36	chr2:97167200-97169400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
37	chr2:97167400-97168000	Enhancers	H1 Cell Line	embryonic stem cell
38	chr2:97167400-97168000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:97167400-97168000	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr2:97167400-97168000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:97167400-97168000	Enhancers	Right Atrium	heart
42	chr2:97167400-97168200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:97167400-97168400	Enhancers	Primary T cells from cord blood	blood
44	chr2:97167400-97169200	Flanking Active TSS	HepG2	liver
45	chr2:97167400-97169400	Enhancers	Left Ventricle	heart
46	chr2:97167400-97169400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr2:97167400-97169600	Enhancers	Fetal Intestine Small	intestine
48	chr2:97167400-97169600	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr2:97167400-97173600	Enhancers	Liver	Liver
50	chr2:97167600-97168000	Bivalent Enhancer	Stomach Smooth Muscle	stomach

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