Variant report

Variant	rs2275001
Chromosome Location	chr1:86913265-86913266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:86913263-86913313	Jurkat	blood:	n/a
2	chr1:86913263-86913313	MCF-7	breast:	n/a
3	chr1:86913263-86913313	HEEpiC	esophagus:	n/a
4	chr1:86913263-86913313	HRCEpiC	kidney:	n/a
5	chr1:86913263-86913313	MCF10A-Er-Src	breast:	n/a
6	chr1:86913263-86913313	NH-A	brain:	n/a
7	chr1:86913263-86913313	HCT-116	colon:	n/a
8	chr1:86913263-86913313	LNCaP	prostate:	n/a
9	chr1:86913263-86913313	AG09319	gingival:	n/a
10	chr1:86913263-86913313	CMK	blood:	n/a
11	chr1:86913263-86913313	HEK293	kidney:	embryo
12	chr1:86913263-86913313	ovcar-3	ovarian:	n/a
13	chr1:86913263-86913313	PrEC	prostate:	n/a
14	chr1:86913263-86913313	HCM	heart:	n/a
15	chr1:86913263-86913313	GM06990	blood:	n/a
16	chr1:86913263-86913313	HRPEpiC	eye:	n/a
17	chr1:86913263-86913313	AG10803	skin:	n/a
18	chr1:86913263-86913313	NB4	blood:	n/a
19	chr1:86913263-86913313	HPAEpiC	pulmonary alveolar:	n/a
20	chr1:86913263-86913313	GM12878	blood:	n/a
21	chr1:86913263-86913313	HIPEpiC	eye:	n/a
22	chr1:86913263-86913313	GM12891	blood:	n/a
23	chr1:86913263-86913313	Hela-S3	cervix:	n/a
24	chr1:86913263-86913313	HCPEpiC	choroid plexus:	n/a
25	chr1:86913263-86913313	SAEC	small airway:	n/a
26	chr1:86913263-86913313	Hepatocyte	liver:	n/a
27	chr1:86913263-86913313	H1-hESC	embryonic stem cell:	embryo
28	chr1:86913263-86913313	HAEpiC	amniotic membrane:	n/a
29	chr1:86913263-86913313	HMEC	breast:	n/a
30	chr1:86913263-86913313	HCF	heart:	n/a
31	chr1:86913263-86913313	HL-60	blood:	n/a
32	chr1:86913263-86913313	AG09309	skin:	n/a
33	chr1:86913263-86913313	IMR90	lung:	fetal
34	chr1:86913263-86913313	SK-N-MC	brain:	n/a
35	chr1:86913263-86913313	NT2-D1	testis:	n/a
36	chr1:86913263-86913313	AG04449	skin:	fetal
37	chr1:86913263-86913313	ECC-1	luminal epithelium:	n/a
38	chr1:86913263-86913313	GM19239	blood:	n/a
39	chr1:86913263-86913313	NHBE	bronchial:	n/a
40	chr1:86913263-86913313	SK-N-SH_RA	brain:	n/a
41	chr1:86913263-86913313	K562	blood:	n/a
42	chr1:86913263-86913313	AoSMC	blood vessel:	n/a
43	chr1:86913263-86913313	HNPCEpiC	eye:	n/a
44	chr1:86913263-86913313	HUVEC	blood vessel:	n/a
45	chr1:86913263-86913313	PANC-1	pancreas:	n/a
46	chr1:86913263-86913313	ProgFib	skin:	n/a
47	chr1:86913263-86913313	T-47D	breast:	n/a
48	chr1:86913263-86913313	GM12892	blood:	n/a
49	chr1:86913263-86913313	BE2_C	brain:	n/a
50	chr1:86913263-86913313	PFSK-1	brain:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86905357..86907939-chr1:86912947..86914769,2	K562	blood:

No data

Variant related genes	Relation type
CLCA2	CpG island
ENSG00000137975	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10873772	0.87[CEU][hapmap]
rs10873778	0.87[CEU][hapmap];0.80[ASN][1000 genomes]
rs1116108	0.87[CEU][hapmap]
rs1116109	0.82[ASN][1000 genomes]
rs11161811	0.83[ASN][1000 genomes]
rs11799437	0.91[CEU][hapmap]
rs11802019	0.84[CEU][hapmap]
rs12033867	0.80[ASN][1000 genomes]
rs12072655	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1407719	0.87[CEU][hapmap]
rs1413427	0.84[CEU][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1413429	0.88[CEU][hapmap];0.85[ASN][1000 genomes]
rs16908	0.87[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17372196	0.87[CEU][hapmap]
rs1999600	0.87[CEU][hapmap];0.82[ASN][1000 genomes]
rs2093612	0.80[ASN][1000 genomes]
rs2210641	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2273941	0.84[CEU][hapmap]
rs2390057	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs2390097	0.87[CEU][hapmap]
rs3737159	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3737672	0.87[CEU][hapmap]
rs3765986	0.92[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3945233	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4656044	0.88[CEU][hapmap]
rs7415758	0.87[CEU][hapmap];0.85[ASN][1000 genomes]
rs7515651	0.83[CEU][hapmap]
rs7553685	0.82[CEU][hapmap];0.83[ASN][1000 genomes]
rs956499	0.88[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9659676	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs969786	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86896600-86914400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:86897200-86922600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:86897200-86922800	Strong transcription	HMEC	breast
4	chr1:86897400-86916000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:86903400-86926800	Weak transcription	Esophagus	oesophagus
6	chr1:86910600-86914400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:86912400-86914800	Strong transcription	NHEK	skin
8	chr1:86912800-86913400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:86912800-86914600	Enhancers	Brain Anterior Caudate	brain
10	chr1:86913200-86913400	Enhancers	Brain Angular Gyrus	brain
11	chr1:86913200-86913400	Enhancers	Brain Cingulate Gyrus	brain
12	chr1:86913200-86913400	Enhancers	Brain Hippocampus Middle	brain
13	chr1:86913200-86913800	Active TSS	Brain Substantia Nigra	brain
14	chr1:86913200-86914600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:86913200-86915600	Enhancers	K562	blood

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