Variant report

Variant	rs2850950
Chromosome Location	chr4:102158450-102158451
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1472826	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17031191	1.00[ASW][hapmap]
rs2119599	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap]
rs2659515	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2659524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2659526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2659528	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850341	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.87[AFR][1000 genomes]
rs2850343	1.00[ASW][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.87[AFR][1000 genomes]
rs2850952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850962	0.87[AFR][1000 genomes]
rs2850965	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.87[AFR][1000 genomes]
rs2850966	0.87[AFR][1000 genomes]
rs2850968	0.87[AFR][1000 genomes]
rs2850973	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.87[AFR][1000 genomes]
rs2851000	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2851006	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2851007	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2851008	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3804397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs756317	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[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
rs2850950	CXXC4	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102146200-102158800	Weak transcription	Gastric	stomach
2	chr4:102146400-102162000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr4:102152200-102159800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:102152400-102158800	Weak transcription	Psoas Muscle	Psoas
5	chr4:102152400-102160200	Weak transcription	Aorta	Aorta
6	chr4:102152800-102165600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:102153000-102165600	Weak transcription	Brain Anterior Caudate	brain
8	chr4:102153000-102165600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:102153800-102159000	Weak transcription	Adipose Nuclei	Adipose
10	chr4:102153800-102159000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr4:102153800-102159000	Weak transcription	NHLF	lung
12	chr4:102153800-102159800	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:102153800-102160000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:102154000-102160200	Weak transcription	HSMM	muscle
15	chr4:102154200-102159000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:102154200-102159600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:102154400-102159000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:102154400-102159000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:102154600-102158800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:102154600-102158800	Weak transcription	Brain Angular Gyrus	brain
21	chr4:102154600-102159000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:102154600-102159600	Weak transcription	HMEC	breast
23	chr4:102154600-102159600	Weak transcription	Osteobl	bone
24	chr4:102154600-102159800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:102154600-102159800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:102154600-102159800	Weak transcription	NHEK	skin
27	chr4:102155000-102158800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:102155200-102160000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:102157400-102159600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:102157400-102160200	Weak transcription	Brain Hippocampus Middle	brain
31	chr4:102157400-102165400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr4:102157600-102159800	Weak transcription	Small Intestine	intestine
33	chr4:102157800-102158800	Weak transcription	Ovary	ovary
34	chr4:102157800-102158800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:102157800-102159200	Enhancers	Stomach Mucosa	stomach
36	chr4:102157800-102159800	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr4:102157800-102159800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr4:102157800-102159800	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr4:102157800-102179600	Weak transcription	Primary B cells from cord blood	blood
40	chr4:102158000-102158800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr4:102158000-102160400	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr4:102158400-102159800	Enhancers	A549	lung
43	chr4:102158400-102161000	Enhancers	Skeletal Muscle Female	skeletal muscle

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