Variant report

Variant	rs721471
Chromosome Location	chr1:86039011-86039012
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:86036311..86039130-chr1:86039970..86042823,4	MCF-7	breast:
2	chr1:86011310..86014222-chr1:86037921..86041658,3	MCF-7	breast:
3	chr1:85964850..85967566-chr1:86038531..86040397,2	MCF-7	breast:
4	chr1:86032809..86034336-chr1:86038823..86041254,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153904	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10493772	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11161638	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1116746	0.82[JPT][hapmap]
rs12034319	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2389969	0.83[MKK][hapmap]
rs3753793	0.84[CHD][hapmap];0.81[MEX][hapmap]
rs3753794	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3753795	0.90[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap];0.85[ASN][1000 genomes]
rs4370804	0.82[JPT][hapmap];0.85[MKK][hapmap]
rs4949911	0.83[MKK][hapmap]
rs7528000	0.90[AMR][1000 genomes];0.90[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
rs721471	CLCA2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86032800-86042000	Weak transcription	Left Ventricle	heart
2	chr1:86034000-86041800	Enhancers	HMEC	breast
3	chr1:86034600-86041400	Weak transcription	Lung	lung
4	chr1:86034800-86041200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:86035200-86041400	Enhancers	HUVEC	blood vessel
6	chr1:86035400-86041000	Genic enhancers	Muscle Satellite Cultured Cells	--
7	chr1:86035400-86041400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:86035400-86041800	Weak transcription	Right Ventricle	heart
9	chr1:86035600-86041800	Weak transcription	Ovary	ovary
10	chr1:86035600-86042000	Weak transcription	Placenta	Placenta
11	chr1:86036200-86040000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:86036200-86041800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:86036200-86042200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:86036400-86041000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:86036400-86041800	Weak transcription	A549	lung
16	chr1:86036600-86041000	Weak transcription	Fetal Heart	heart
17	chr1:86036600-86041200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:86036800-86041800	Enhancers	Hela-S3	cervix
19	chr1:86037000-86040600	Genic enhancers	NHLF	lung
20	chr1:86037000-86040800	Genic enhancers	HSMM	muscle
21	chr1:86037400-86039200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:86037400-86040200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:86037400-86041800	Weak transcription	Fetal Kidney	kidney
24	chr1:86037800-86039400	Genic enhancers	Osteobl	bone
25	chr1:86037800-86041200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:86037800-86041200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:86037800-86041200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:86037800-86042000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:86038000-86039800	Weak transcription	HepG2	liver
30	chr1:86038000-86040000	Genic enhancers	NH-A	brain
31	chr1:86038000-86040400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:86038000-86041800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:86038200-86040200	Enhancers	NHDF-Ad	bronchial
34	chr1:86038200-86040600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:86038400-86039200	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr1:86038400-86040600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:86038600-86039200	Weak transcription	Aorta	Aorta
38	chr1:86038600-86039200	Weak transcription	HSMMtube	muscle
39	chr1:86038600-86039800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:86038600-86040000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:86038600-86040400	Enhancers	NHEK	skin
42	chr1:86038600-86041800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:86038600-86041800	Weak transcription	Fetal Stomach	stomach
44	chr1:86038600-86042000	Weak transcription	Esophagus	oesophagus
45	chr1:86038600-86042000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:86038800-86039400	Enhancers	Adipose Nuclei	Adipose
47	chr1:86039000-86040000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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