Variant report

Variant	rs4370804
Chromosome Location	chr1:86052985-86052986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85931646..85934591-chr1:86050681..86053602,2	MCF-7	breast:
2	chr1:86051548..86054747-chr1:86058941..86061467,3	K562	blood:

Variant related genes	Relation type
ENSG00000273264	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10493772	0.82[JPT][hapmap]
rs10873708	0.81[CHD][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap]
rs10873710	0.85[LWK][hapmap];1.00[YRI][hapmap]
rs1116746	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11578464	0.85[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs12120700	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2389969	0.92[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3753794	0.82[EUR][1000 genomes]
rs4949896	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4949910	0.99[ASN][1000 genomes]
rs4949911	0.83[ASW][hapmap];0.95[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4949912	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4949914	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4949915	0.82[YRI][hapmap]
rs721471	0.82[JPT][hapmap];0.85[MKK][hapmap]
rs9658595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4370804	CLCA2	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86048600-86053400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:86048800-86053600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:86048800-86081200	Weak transcription	Gastric	stomach
4	chr1:86049000-86053600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:86049000-86053600	Weak transcription	Fetal Intestine Small	intestine
6	chr1:86049000-86068400	Weak transcription	Psoas Muscle	Psoas
7	chr1:86049200-86053200	Weak transcription	Left Ventricle	heart
8	chr1:86049200-86053600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:86049400-86053200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:86049400-86053600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:86049400-86053600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:86050200-86053400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:86050200-86053600	Weak transcription	Adipose Nuclei	Adipose
14	chr1:86050200-86053600	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:86050600-86053400	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:86050600-86053600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:86050600-86054800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:86050800-86053600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:86050800-86053600	Weak transcription	Fetal Stomach	stomach
20	chr1:86051000-86053200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:86051000-86053200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:86051000-86053400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:86051000-86053600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:86051000-86053600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:86051000-86053600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:86051000-86053600	Weak transcription	Fetal Lung	lung
27	chr1:86051000-86062800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:86051200-86054400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:86051800-86053400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:86051800-86053400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:86051800-86053400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:86051800-86053400	Weak transcription	A549	lung
33	chr1:86051800-86053600	Weak transcription	NH-A	brain
34	chr1:86052000-86053200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:86052000-86053200	Weak transcription	Fetal Heart	heart
36	chr1:86052000-86053400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:86052000-86053400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:86052000-86053600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:86052000-86053600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:86052000-86053600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:86052000-86053600	Weak transcription	NHLF	lung
42	chr1:86052200-86053000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:86052200-86053400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:86052200-86053400	Weak transcription	NHDF-Ad	bronchial
45	chr1:86052200-86054000	Enhancers	Fetal Brain Male	brain
46	chr1:86052200-86055000	Weak transcription	Osteobl	bone
47	chr1:86052800-86053200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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