Variant report

Variant	rs3731940
Chromosome Location	chr2:97377883-97377884
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	POLR2A	chr2:97377688-97378002	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:97377199..97379924-chr2:97404975..97407018,2	MCF-7	breast:
2	chr2:97360914..97363341-chr2:97377649..97380525,2	MCF-7	breast:

Variant related genes	Relation type
LMAN2L	TF binding region
ENSG00000114988	Chromatin interaction
ENSG00000249715	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1320146	1.00[GIH][hapmap]
rs17119562	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17119564	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17119591	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs17119598	1.00[ASW][hapmap];1.00[GIH][hapmap]
rs2139406	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes]
rs2276654	1.00[ASW][hapmap];1.00[GIH][hapmap]
rs2280356	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs2314399	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2872633	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3731941	1.00[ASW][hapmap];1.00[GIH][hapmap];0.81[YRI][hapmap]
rs56797569	0.81[ASN][1000 genomes]
rs56913233	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57582887	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59073958	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59648446	0.88[EUR][1000 genomes]
rs61742095	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61750875	0.90[EUR][1000 genomes]
rs62152765	0.81[ASN][1000 genomes]
rs62152766	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62152767	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62152768	0.81[ASN][1000 genomes]
rs62152770	0.81[ASN][1000 genomes]
rs62152771	1.00[EUR][1000 genomes]
rs62152780	1.00[EUR][1000 genomes]
rs62152787	1.00[EUR][1000 genomes]
rs62156206	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62156207	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62156208	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62156209	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62156210	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62156211	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62156212	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62156213	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62156216	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62156219	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62156220	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62156221	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62156222	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62156223	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62156225	0.81[ASN][1000 genomes]
rs62156226	0.81[ASN][1000 genomes]
rs62156227	0.81[ASN][1000 genomes]
rs62156228	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62156230	0.81[ASN][1000 genomes]
rs62156231	0.81[ASN][1000 genomes]
rs62156232	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62156233	0.81[ASN][1000 genomes]
rs62156234	0.81[ASN][1000 genomes]
rs6576981	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6576987	1.00[GIH][hapmap]
rs6751132	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6753987	1.00[GIH][hapmap]
rs6758151	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs7568206	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7580942	1.00[GIH][hapmap]
rs9948	1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 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
11	nsv469775	chr2:97240926-97412491	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv482586	chr2:97240926-97412491	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv834306	chr2:97241115-97412938	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
14	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
15	nsv834307	chr2:97321447-97479266	Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97360800-97381200	Strong transcription	Fetal Stomach	stomach
2	chr2:97362800-97379800	Strong transcription	Fetal Intestine Large	intestine
3	chr2:97365000-97389400	Strong transcription	Fetal Muscle Trunk	muscle
4	chr2:97365200-97387000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:97365400-97382400	Strong transcription	Primary T cells from cord blood	blood
6	chr2:97365600-97380400	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:97366000-97379800	Strong transcription	Fetal Muscle Leg	muscle
8	chr2:97366800-97380200	Strong transcription	Stomach Smooth Muscle	stomach
9	chr2:97367200-97378000	Strong transcription	Colonic Mucosa	Colon
10	chr2:97367400-97380200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:97367400-97382600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:97367600-97378600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:97367600-97381000	Strong transcription	HepG2	liver
14	chr2:97367800-97378000	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:97367800-97378800	Strong transcription	Lung	lung
16	chr2:97367800-97379000	Strong transcription	Rectal Smooth Muscle	rectum
17	chr2:97367800-97379400	Strong transcription	Right Ventricle	heart
18	chr2:97367800-97379800	Strong transcription	Duodenum Mucosa	Duodenum
19	chr2:97367800-97380000	Strong transcription	Liver	Liver
20	chr2:97367800-97380200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:97367800-97382800	Strong transcription	Brain Anterior Caudate	brain
22	chr2:97368000-97379600	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr2:97368000-97380200	Strong transcription	Ovary	ovary
24	chr2:97368200-97379200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:97368200-97379400	Strong transcription	Placenta	Placenta
26	chr2:97368200-97382600	Strong transcription	Fetal Thymus	thymus
27	chr2:97368400-97379400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:97368400-97405000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:97368600-97379000	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr2:97368600-97383200	Strong transcription	Brain Cingulate Gyrus	brain
31	chr2:97370000-97378600	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:97370000-97379000	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:97370000-97380000	Strong transcription	Left Ventricle	heart
34	chr2:97370000-97380200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:97370200-97378000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:97370200-97380200	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr2:97370200-97382400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr2:97370400-97378200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:97370400-97379000	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:97370400-97379600	Strong transcription	Primary B cells from peripheral blood	blood
41	chr2:97370400-97380400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:97370600-97378000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr2:97370600-97378000	Strong transcription	NHEK	skin
44	chr2:97370600-97378200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:97370600-97378600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:97370600-97378600	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr2:97370600-97378800	Strong transcription	Dnd41	blood
48	chr2:97370600-97379200	Strong transcription	Esophagus	oesophagus
49	chr2:97370600-97380600	Strong transcription	Adipose Nuclei	Adipose
50	chr2:97370600-97398800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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