Variant report

Variant	rs13142024
Chromosome Location	chr4:102089849-102089850
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102088927..102090485-chr4:102267393..102270009,2	MCF-7	breast:
2	chr4:102086824..102091694-chr4:102266945..102270646,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138814	Chromatin interaction
ENSG00000254531	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10005338	0.85[EUR][1000 genomes]
rs10018021	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10025780	0.85[EUR][1000 genomes]
rs10030389	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10050301	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs10516471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13103902	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13111186	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13112866	0.92[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs13118966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13125501	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13128841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13135924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1810024	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1880943	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2048072	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2063058	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2174680	0.84[EUR][1000 genomes]
rs2659552	0.81[EUR][1000 genomes]
rs2695215	1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs2695217	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2695219	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs3804361	0.85[EUR][1000 genomes]
rs3804368	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs3811063	0.89[CEU][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs3827770	0.81[EUR][1000 genomes]
rs4590038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698912	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4698913	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699106	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699116	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs4699127	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs7677550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs950177	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9884638	0.84[EUR][1000 genomes]
rs9995338	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13142024	CXXC4	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102062600-102090400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:102078400-102093200	Weak transcription	HUVEC	blood vessel
3	chr4:102078400-102096600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:102078600-102090200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr4:102078800-102096000	Weak transcription	Ovary	ovary
6	chr4:102079400-102113800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr4:102079800-102096400	Weak transcription	Adipose Nuclei	Adipose
8	chr4:102080000-102092200	Weak transcription	NHDF-Ad	bronchial
9	chr4:102080000-102092600	Weak transcription	NH-A	brain
10	chr4:102080600-102093000	Weak transcription	NHLF	lung
11	chr4:102080600-102100600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:102081000-102090200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:102082600-102090000	Weak transcription	Primary B cells from cord blood	blood
14	chr4:102083000-102096200	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:102083200-102096800	Weak transcription	Brain Angular Gyrus	brain
16	chr4:102084200-102103400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr4:102084800-102090200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr4:102084800-102092000	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:102085400-102090400	Weak transcription	Esophagus	oesophagus
20	chr4:102085400-102094200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:102085600-102096600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:102087200-102090600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr4:102087200-102090600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:102087400-102090600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:102087600-102090200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:102087600-102090200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:102087600-102093200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:102087600-102096400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr4:102087800-102092400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:102088000-102094400	Enhancers	A549	lung
31	chr4:102088200-102090400	Enhancers	Duodenum Mucosa	Duodenum
32	chr4:102088200-102090600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:102088200-102091000	Enhancers	HepG2	liver
34	chr4:102088200-102093000	Enhancers	Stomach Mucosa	stomach
35	chr4:102088400-102093000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:102088800-102090800	Enhancers	Fetal Intestine Small	intestine
37	chr4:102088800-102091400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr4:102088800-102094800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:102089000-102097600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr4:102089200-102090200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:102089200-102090200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr4:102089200-102090600	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr4:102089200-102092600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:102089200-102097000	Weak transcription	Psoas Muscle	Psoas
45	chr4:102089200-102097200	Weak transcription	Pancreas	Pancrea
46	chr4:102089400-102090400	Weak transcription	Brain Anterior Caudate	brain
47	chr4:102089400-102090800	Enhancers	Fetal Intestine Large	intestine
48	chr4:102089600-102090000	Weak transcription	Brain Substantia Nigra	brain
49	chr4:102089600-102092600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr4:102089800-102090200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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