Variant report

Variant	rs3923144
Chromosome Location	chr2:39103991-39103992
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	HCFC1	chr2:39102166-39104264	Hela-S3	cervix:	n/a	n/a
2	JUND	chr2:39102239-39104280	SK-N-SH	brain:	n/a	chr2:39103073-39103082
3	MAFK	chr2:39103945-39103994	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:39103964-39104074	MCF10A-Er-Src	breast:	n/a	n/a
5	MXI1	chr2:39101863-39104341	SK-N-SH	brain:	n/a	chr2:39103127-39103142 chr2:39102329-39102338
6	SREBP1	chr2:39101910-39104141	GM12878	blood:	n/a	chr2:39103128-39103142 chr2:39103701-39103711

No.	Distal block	Cell Line	Cell type
1	chr2:38976877..38979785-chr2:39100480..39105632,13	K562	blood:
2	chr2:38976936..38979845-chr2:39101241..39105632,7	K562	blood:
3	chr2:39097841..39100728-chr2:39103293..39104847,2	MCF-7	breast:

Variant related genes	Relation type
DHX57	TF binding region
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1010859	0.90[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap]
rs10779923	0.82[GIH][hapmap]
rs11124653	0.82[EUR][1000 genomes]
rs11124655	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11681583	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11689954	0.85[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12617734	0.85[EUR][1000 genomes]
rs12712625	0.81[GIH][hapmap];0.87[JPT][hapmap]
rs12712626	0.90[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs12712627	0.81[GIH][hapmap];0.87[JPT][hapmap]
rs13029388	0.87[JPT][hapmap]
rs1901289	0.81[GIH][hapmap]
rs2060743	0.89[CEU][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2060744	0.82[AMR][1000 genomes]
rs2373467	0.87[LWK][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes]
rs2373473	0.84[EUR][1000 genomes]
rs3099945	0.82[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs3099946	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3099948	0.90[EUR][1000 genomes]
rs3099949	0.90[EUR][1000 genomes]
rs3099956	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs3099957	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs3099958	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs3100000	0.82[CHB][hapmap]
rs3112159	0.90[CHB][hapmap];0.82[GIH][hapmap]
rs3112163	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap]
rs3112170	0.88[EUR][1000 genomes]
rs3112171	0.85[EUR][1000 genomes]
rs3112172	0.85[EUR][1000 genomes]
rs373300	0.86[MEX][hapmap]
rs4670266	0.90[CHB][hapmap]
rs4670899	0.88[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes]
rs4670900	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6706186	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6738069	0.88[CHD][hapmap];0.88[GIH][hapmap]
rs7565111	0.90[CHB][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7586929	0.83[ASN][1000 genomes]
rs7598922	0.81[GIH][hapmap]
rs8179664	0.81[CEU][hapmap];0.80[CHB][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv2692	chr2:39065768-39111871	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3923144	MORN2	cis	parietal	SCAN
rs3923144	DHX57	cis	cerebellum	SCAN
rs3923144	ITGB1	trans	parietal	SCAN
rs3923144	DHX57	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39101800-39104200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:39101800-39104200	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr2:39102000-39104000	Active TSS	H1 Cell Line	embryonic stem cell
4	chr2:39102000-39104000	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr2:39102000-39104000	Active TSS	Muscle Satellite Cultured Cells	--
6	chr2:39102000-39104200	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr2:39102000-39104200	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr2:39102000-39104200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr2:39102200-39104000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:39102200-39104000	Active TSS	Ovary	ovary
11	chr2:39102400-39104000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:39102400-39104200	Active TSS	Rectal Smooth Muscle	rectum
13	chr2:39102400-39104200	Active TSS	HSMM	muscle
14	chr2:39102600-39104000	Active TSS	Fetal Kidney	kidney
15	chr2:39103200-39104000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr2:39103200-39104000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:39103200-39104000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr2:39103200-39104000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:39103200-39104000	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr2:39103200-39104000	Flanking Active TSS	Liver	Liver
21	chr2:39103200-39104000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr2:39103200-39104200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:39103400-39104000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:39103400-39104000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr2:39103400-39104000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:39103400-39104000	Flanking Active TSS	Brain Germinal Matrix	brain
27	chr2:39103400-39104000	Flanking Active TSS	Brain Hippocampus Middle	brain
28	chr2:39103400-39104000	Flanking Active TSS	Colonic Mucosa	Colon
29	chr2:39103400-39104000	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr2:39103400-39104000	Flanking Active TSS	Fetal Brain Male	brain
31	chr2:39103400-39104000	Flanking Active TSS	Psoas Muscle	Psoas
32	chr2:39103400-39104000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr2:39103400-39104000	Flanking Active TSS	Right Ventricle	heart
34	chr2:39103400-39104000	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr2:39103400-39104000	Flanking Active TSS	Thymus	Thymus
36	chr2:39103400-39104000	Flanking Active TSS	HUVEC	blood vessel
37	chr2:39103400-39104000	Flanking Active TSS	NH-A	brain
38	chr2:39103400-39104200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:39103400-39104200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:39103400-39104200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:39103400-39104200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr2:39103400-39104200	Flanking Active TSS	Dnd41	blood
43	chr2:39103600-39104000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:39103600-39104000	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr2:39103600-39104000	Enhancers	Primary B cells from peripheral blood	blood
46	chr2:39103600-39104000	Flanking Active TSS	Brain Angular Gyrus	brain
47	chr2:39103600-39104000	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr2:39103600-39104000	Flanking Active TSS	Brain Substantia Nigra	brain
49	chr2:39103600-39104000	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr2:39103600-39104000	Flanking Active TSS	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links