Variant report

Variant	rs2235543
Chromosome Location	chr1:209860668-209860669
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10082169	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10082248	0.81[CHB][hapmap]
rs12565406	0.87[CEU][hapmap]
rs3753519	0.95[CHB][hapmap]
rs760951	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs760952	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2235543	C4BPA	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209849600-209861400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209849800-209862000	Weak transcription	NHLF	lung
3	chr1:209857400-209861400	Weak transcription	HMEC	breast
4	chr1:209858400-209860800	Enhancers	Ovary	ovary
5	chr1:209858800-209862600	Enhancers	Fetal Heart	heart
6	chr1:209858800-209863000	Enhancers	Fetal Stomach	stomach
7	chr1:209858800-209863400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:209859000-209860800	Enhancers	Fetal Kidney	kidney
9	chr1:209859000-209863200	Enhancers	Right Atrium	heart
10	chr1:209859200-209862400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:209859200-209862800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:209859200-209863000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:209859200-209863200	Enhancers	Fetal Muscle Leg	muscle
14	chr1:209859400-209861600	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:209859400-209862400	Weak transcription	Stomach Mucosa	stomach
16	chr1:209859400-209862600	Weak transcription	Adipose Nuclei	Adipose
17	chr1:209859400-209863000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:209859400-209866000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:209859600-209861800	Enhancers	Primary T cells fromperipheralblood	blood
20	chr1:209859600-209861800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:209859600-209861800	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr1:209859600-209861800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:209859600-209862200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:209859600-209862400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr1:209859600-209862400	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr1:209859600-209866000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:209860000-209860800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:209860200-209862400	Enhancers	Rectal Smooth Muscle	rectum
29	chr1:209860200-209862800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:209860200-209863600	Enhancers	Left Ventricle	heart
31	chr1:209860400-209861000	Flanking Active TSS	HSMMtube	muscle
32	chr1:209860400-209861400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:209860400-209861400	Weak transcription	Right Ventricle	heart
34	chr1:209860400-209861600	Enhancers	Primary T cells from cord blood	blood
35	chr1:209860600-209861600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr1:209860600-209861600	Weak transcription	Fetal Lung	lung
37	chr1:209860600-209862600	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr1:209860600-209862600	Enhancers	HSMM	muscle

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