Variant report

Variant	rs3823842
Chromosome Location	chr7:7604913-7604914
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr7:7604702-7604935	K562	blood:	n/a	n/a
2	ATF1	chr7:7604647-7605005	K562	blood:	n/a	n/a
3	SMARCC1	chr7:7603662-7604948	Hela-S3	cervix:	n/a	n/a
4	RCOR1	chr7:7604585-7605090	K562	blood:	n/a	n/a
5	RCOR1	chr7:7604780-7604930	K562	blood:	n/a	n/a
6	NR2F2	chr7:7604670-7605034	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:7604819..7606875-chr7:8300807..8302647,2	MCF-7	breast:
2	chr7:7588099..7594648-chr7:7604621..7611487,9	MCF-7	breast:
3	chr7:7603096..7605323-chr7:7605419..7606942,2	MCF-7	breast:
4	chr7:7603046..7608569-chr7:7677123..7682101,8	MCF-7	breast:

No data

Variant related genes	Relation type
MIOS	TF binding region
ENSG00000272894	TF binding region
ENSG00000003147	Chromatin interaction
ENSG00000219545	Chromatin interaction
ENSG00000272894	Chromatin interaction
ENSG00000164654	Chromatin interaction
ENSG00000106399	Chromatin interaction
ENSG00000229970	Chromatin interaction
ENSG00000272732	Chromatin interaction
ENSG00000244239	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10227453	0.94[CHB][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10236767	1.00[CEU][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs10486174	0.92[CEU][hapmap]
rs10486178	0.94[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10486179	0.92[CEU][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap]
rs10486182	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs10952061	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11767285	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11771272	0.81[EUR][1000 genomes]
rs11975180	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs12532693	0.93[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12533006	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13244586	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13312659	0.92[CEU][hapmap]
rs1544465	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs1544466	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17151557	0.94[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs17168408	0.94[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs17168446	0.83[ASN][1000 genomes]
rs17168463	0.94[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs17168516	0.94[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.83[ASN][1000 genomes]
rs1971649	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2023999	0.94[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2108066	0.94[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2108069	0.87[EUR][1000 genomes]
rs2214842	0.83[ASN][1000 genomes]
rs2286209	0.84[CEU][hapmap]
rs2348337	0.87[EUR][1000 genomes]
rs2348338	0.89[EUR][1000 genomes]
rs28483212	0.82[ASN][1000 genomes]
rs28553401	0.83[ASN][1000 genomes]
rs3807856	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3815229	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4720740	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4724999	0.81[CEU][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap]
rs4725000	0.96[CEU][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap]
rs56412915	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60498098	0.83[ASN][1000 genomes]
rs6943655	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6966277	0.80[CEU][hapmap]
rs6968507	0.96[CEU][hapmap];0.80[GIH][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6977450	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6977577	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6977800	0.92[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs720288	0.82[ASN][1000 genomes]
rs73674573	0.81[ASN][1000 genomes]
rs73674574	0.83[ASN][1000 genomes]
rs73674578	0.82[ASN][1000 genomes]
rs73674581	0.90[ASN][1000 genomes]
rs73674582	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7459399	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7778306	0.92[CEU][hapmap]
rs7779415	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7784747	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7796700	0.92[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs7803888	1.00[CEU][hapmap];0.89[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv887470	chr7:7310023-7655094	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv887472	chr7:7405069-7680697	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv887473	chr7:7497676-7604913	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv887474	chr7:7519603-7679644	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv887475	chr7:7519603-7679644	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
11	nsv887476	chr7:7519603-7680697	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
13	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
14	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3823842	COL28A1	cis	temporal cortex	BrainEAC
rs3823842	COL28A1	cis	cerebellar cortex	BrainEAC
rs3823842	COL28A1	cis	cerebellum	SCAN
rs3823842	COL28A1	cis	parietal	SCAN
rs3823842	AIMP2	cis	parietal	SCAN
rs3823842	COL28A1	cis	brain	BrainEAC
rs3823842	COL28A1	cis	lung	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7589400-7605800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr7:7590000-7606000	Weak transcription	Brain Substantia Nigra	brain
3	chr7:7590000-7606200	Weak transcription	Ovary	ovary
4	chr7:7590200-7605800	Weak transcription	Brain Anterior Caudate	brain
5	chr7:7590200-7605800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr7:7593800-7606000	Weak transcription	Right Atrium	heart
7	chr7:7595800-7605600	Weak transcription	Fetal Kidney	kidney
8	chr7:7597000-7605400	Weak transcription	Lung	lung
9	chr7:7597200-7606600	Weak transcription	Gastric	stomach
10	chr7:7597800-7606000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr7:7599200-7605800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr7:7600000-7606000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr7:7601600-7605000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:7602200-7605800	Enhancers	Liver	Liver
15	chr7:7602400-7605800	Enhancers	Stomach Mucosa	stomach
16	chr7:7602600-7605000	Enhancers	Placenta	Placenta
17	chr7:7602800-7606400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr7:7603000-7605200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr7:7603000-7605800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr7:7603400-7606000	Enhancers	HMEC	breast
21	chr7:7603600-7605400	Enhancers	NHDF-Ad	bronchial
22	chr7:7603600-7605800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr7:7603600-7606200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr7:7603600-7606400	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr7:7603800-7605400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:7603800-7605400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:7603800-7605400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:7603800-7605800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:7603800-7605800	Weak transcription	HepG2	liver
30	chr7:7603800-7606000	Weak transcription	Brain Hippocampus Middle	brain
31	chr7:7603800-7606000	Enhancers	HSMM	muscle
32	chr7:7604000-7605000	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr7:7604000-7605800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr7:7604200-7605800	Weak transcription	Psoas Muscle	Psoas
35	chr7:7604200-7606000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr7:7604200-7606000	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr7:7604200-7606200	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr7:7604200-7607800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:7604400-7605200	Enhancers	NHEK	skin
40	chr7:7604400-7605400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr7:7604400-7605600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr7:7604400-7605800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr7:7604400-7605800	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr7:7604400-7606000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:7604400-7606000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr7:7604400-7606000	Enhancers	Esophagus	oesophagus
47	chr7:7604400-7606200	Enhancers	Placenta Amnion	Placenta Amnion
48	chr7:7604600-7605000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr7:7604600-7605800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr7:7604600-7605800	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links