Variant report

Variant	rs950177
Chromosome Location	chr4:102098573-102098574
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10005338	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10018021	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10025780	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10030389	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10050301	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10516471	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13103902	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13111186	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13112866	0.89[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs13118966	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13125501	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13128841	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13135924	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13142024	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]
rs1810024	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1880943	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs2048072	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs2063058	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs2174680	0.86[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];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs2695219	0.86[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs3804361	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3804368	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3811063	0.92[CEU][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs3827770	0.83[EUR][1000 genomes]
rs4590038	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4698912	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4698913	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699106	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699116	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4699127	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7677550	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];0.97[ASN][1000 genomes]
rs9884638	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9995338	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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
rs950177	CXXC4	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102079400-102113800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr4:102080600-102100600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:102084200-102103400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:102090400-102103800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr4:102090800-102099400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr4:102090800-102112200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:102090800-102114400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:102091200-102103400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr4:102091400-102103600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr4:102093400-102100400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:102093400-102103800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:102093600-102103800	Weak transcription	NHEK	skin
13	chr4:102093600-102105200	Weak transcription	NHLF	lung
14	chr4:102093800-102099800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:102094400-102099600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:102094400-102099600	Weak transcription	NHDF-Ad	bronchial
17	chr4:102094400-102103800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:102094400-102108600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:102094600-102100200	Weak transcription	Osteobl	bone
20	chr4:102095800-102098600	Enhancers	Colon Smooth Muscle	Colon
21	chr4:102095800-102098600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr4:102095800-102099000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:102095800-102099400	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr4:102095800-102103600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr4:102096200-102112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:102096400-102098600	Enhancers	Rectal Smooth Muscle	rectum
27	chr4:102096600-102099200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:102096600-102099800	Enhancers	Brain Anterior Caudate	brain
29	chr4:102096600-102112000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr4:102096600-102112000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:102096600-102112000	Weak transcription	Right Ventricle	heart
32	chr4:102096800-102098600	Enhancers	HepG2	liver
33	chr4:102096800-102099600	Enhancers	HUVEC	blood vessel
34	chr4:102096800-102103400	Weak transcription	Primary B cells from cord blood	blood
35	chr4:102096800-102108000	Weak transcription	Brain Hippocampus Middle	brain
36	chr4:102097000-102098600	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr4:102097000-102098600	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr4:102097000-102098800	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr4:102097000-102100400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr4:102097000-102103600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr4:102097400-102098600	Weak transcription	Gastric	stomach
42	chr4:102097400-102103200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:102097400-102112200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr4:102097600-102098600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr4:102097600-102103400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:102097600-102105000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr4:102097800-102101200	Weak transcription	Psoas Muscle	Psoas
48	chr4:102097800-102101200	Weak transcription	Right Atrium	heart
49	chr4:102097800-102101200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr4:102097800-102103600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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