Variant report

Variant	rs391984
Chromosome Location	chr2:40478414-40478415
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	REST	chr2:40477998-40479015	H1-neurons	neurons:	n/a	n/a
2	MAX	chr2:40478387-40478595	H1-hESC	embryonic stem cell:	n/a	n/a
3	REST	chr2:40478302-40478744	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr2:40478221-40478991	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr2:40478240-40478699	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
SLC8A1-AS1	TF binding region

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs105288	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1641452	0.85[ASN][1000 genomes]
rs1641458	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1651356	0.89[ASN][1000 genomes]
rs34971853	0.96[ASN][1000 genomes]
rs36162999	0.93[ASN][1000 genomes]
rs36184451	0.82[ASN][1000 genomes]
rs366578	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs368642	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs369140	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs371909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs372052	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs373606	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs374159	0.85[ASN][1000 genomes]
rs3749056	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs379410	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs379859	0.91[ASN][1000 genomes]
rs380082	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs380975	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs383073	0.93[ASN][1000 genomes]
rs384511	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs384994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs385561	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs389109	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs389992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs391631	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs393711	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs394112	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs394540	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs395404	0.81[JPT][hapmap]
rs398175	0.86[ASN][1000 genomes]
rs399061	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs401815	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs402307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs405884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs406222	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs406736	0.85[ASN][1000 genomes]
rs406880	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs407267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs407388	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs407889	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs408009	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs413711	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs415695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs417464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs417591	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs417873	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs418780	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs421870	1.00[JPT][hapmap]
rs426295	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs427632	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs428738	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs429227	0.85[ASN][1000 genomes]
rs430314	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs430394	0.82[ASN][1000 genomes]
rs432142	0.81[ASN][1000 genomes]
rs432769	1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432981	0.85[ASN][1000 genomes]
rs434082	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs436010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs439960	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs440155	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs441196	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs441413	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs441593	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs442476	0.85[ASN][1000 genomes]
rs442586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs443236	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs444504	0.81[ASN][1000 genomes]
rs450116	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs450823	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs451074	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs451158	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs451811	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs452138	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs479909	0.82[ASN][1000 genomes]
rs4952596	0.93[ASN][1000 genomes]
rs505473	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs581477	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs581568	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs588179	0.90[ASN][1000 genomes]
rs615449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs666362	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs674128	0.88[ASN][1000 genomes]
rs678107	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs679339	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs688673	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs72794789	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv1851152	chr2:40393223-40512023	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1008190	chr2:40429442-40506772	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv34071	chr2:40435231-40578229	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv524586	chr2:40447587-40497501	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv873912	chr2:40468418-40492315	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv873913	chr2:40469705-40485074	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40448000-40487400	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr2:40451400-40490000	Weak transcription	Dnd41	blood
3	chr2:40467800-40487400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:40470400-40481200	Weak transcription	Brain Germinal Matrix	brain
5	chr2:40472200-40478600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:40472600-40487200	Weak transcription	HSMM	muscle
7	chr2:40475800-40478600	Enhancers	Hela-S3	cervix
8	chr2:40475800-40480000	Enhancers	Fetal Heart	heart
9	chr2:40475800-40485400	Weak transcription	Right Atrium	heart
10	chr2:40477200-40478800	Enhancers	Rectal Smooth Muscle	rectum
11	chr2:40477600-40479000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:40477600-40479200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:40477800-40479400	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr2:40477800-40479600	Enhancers	Colon Smooth Muscle	Colon
15	chr2:40477800-40479800	Enhancers	Fetal Intestine Small	intestine
16	chr2:40477800-40479800	Enhancers	Stomach Mucosa	stomach
17	chr2:40478000-40478800	Enhancers	Fetal Stomach	stomach
18	chr2:40478000-40478800	Enhancers	Placenta Amnion	Placenta Amnion
19	chr2:40478000-40479400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:40478000-40479600	Enhancers	Primary hematopoietic stem cells	blood
21	chr2:40478000-40479800	Enhancers	Fetal Intestine Large	intestine
22	chr2:40478200-40478800	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr2:40478200-40479200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:40478400-40478600	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr2:40478400-40478800	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr2:40478400-40478800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr2:40478400-40478800	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr2:40478400-40478800	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr2:40478400-40478800	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr2:40478400-40478800	Enhancers	Right Ventricle	heart
31	chr2:40478400-40479000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:40478400-40479800	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links