Variant report

Variant	rs12625552
Chromosome Location	chr20:16408272-16408273
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:16407115..16409066-chr20:16429669..16431303,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12624939	1.00[CHB][hapmap]
rs1884604	1.00[CHB][hapmap]
rs1884605	1.00[CHB][hapmap]
rs1884606	1.00[CHB][hapmap]
rs2093004	1.00[CHB][hapmap]
rs2144883	1.00[CHB][hapmap]
rs2180442	1.00[CHB][hapmap]
rs2208059	1.00[CHB][hapmap]
rs2328017	1.00[CHB][hapmap]
rs2328018	1.00[CHB][hapmap]
rs4814469	1.00[CHB][hapmap]
rs6034438	1.00[CHB][hapmap]
rs6034439	1.00[CHB][hapmap]
rs6034446	1.00[CHB][hapmap]
rs6034447	1.00[CHB][hapmap]
rs6034460	1.00[CHB][hapmap]
rs6034461	1.00[CHB][hapmap]
rs6034487	1.00[CHB][hapmap]
rs6043852	1.00[CHB][hapmap]
rs6043854	1.00[CHB][hapmap]
rs6043858	1.00[CHB][hapmap]
rs6043870	1.00[CHB][hapmap]
rs6043879	1.00[CHB][hapmap]
rs6043881	1.00[CHB][hapmap]
rs6043882	1.00[CHB][hapmap]
rs6043887	1.00[CHB][hapmap]
rs6043892	1.00[CHB][hapmap]
rs6105582	1.00[CHB][hapmap]
rs6105603	1.00[CHB][hapmap]
rs7271622	1.00[CHB][hapmap]
rs8117949	1.00[CHB][hapmap]
rs8119246	1.00[CHB][hapmap]
rs8122535	1.00[CHB][hapmap]

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	nsv833931	chr20:16308276-16460596	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12625552	C20orf23	cis	multi-tissue	Pritchard

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16384000-16432600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr20:16387400-16411800	Weak transcription	Colonic Mucosa	Colon
3	chr20:16391600-16410800	Weak transcription	Thymus	Thymus
4	chr20:16391800-16409800	Weak transcription	Brain Angular Gyrus	brain
5	chr20:16391800-16414600	Weak transcription	Colon Smooth Muscle	Colon
6	chr20:16392200-16412800	Weak transcription	Fetal Kidney	kidney
7	chr20:16392200-16453000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr20:16392400-16411600	Weak transcription	Brain Substantia Nigra	brain
9	chr20:16395200-16411400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr20:16396000-16411400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr20:16396200-16412800	Weak transcription	NHDF-Ad	bronchial
12	chr20:16396400-16411000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr20:16397400-16412000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr20:16398200-16417000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr20:16398200-16431000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr20:16400000-16440000	Weak transcription	NHEK	skin
17	chr20:16400200-16414000	Weak transcription	Fetal Brain Female	brain
18	chr20:16401000-16414200	Weak transcription	Fetal Brain Male	brain
19	chr20:16401200-16417000	Weak transcription	Brain Germinal Matrix	brain
20	chr20:16402600-16410200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr20:16402600-16412200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr20:16402800-16412800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr20:16402800-16412800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr20:16402800-16413600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr20:16403000-16413000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr20:16403200-16408600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr20:16403200-16409200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr20:16403200-16409200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr20:16403600-16410600	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr20:16404000-16410200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr20:16404000-16410200	Strong transcription	Duodenum Mucosa	Duodenum
32	chr20:16404000-16410800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr20:16404000-16411000	Strong transcription	Adipose Nuclei	Adipose
34	chr20:16404200-16408600	Strong transcription	Fetal Intestine Small	intestine
35	chr20:16404200-16409600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr20:16404200-16410200	Strong transcription	Fetal Intestine Large	intestine
37	chr20:16404200-16410200	Strong transcription	Left Ventricle	heart
38	chr20:16404200-16410200	Strong transcription	Ovary	ovary
39	chr20:16404200-16411200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr20:16404200-16411400	Strong transcription	Primary T cells from cord blood	blood
41	chr20:16404200-16419200	Weak transcription	Fetal Heart	heart
42	chr20:16404400-16410000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr20:16404400-16410200	Strong transcription	Esophagus	oesophagus
44	chr20:16404400-16410200	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr20:16404400-16410400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr20:16404600-16408600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr20:16404600-16410600	Strong transcription	Stomach Smooth Muscle	stomach
48	chr20:16404600-16411200	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr20:16404600-16414000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr20:16404800-16408400	Weak transcription	Gastric	stomach

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