Variant report

Variant	rs17035146
Chromosome Location	chr12:104442938-104442939
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104440677..104443075-chr12:104444552..104446147,2	K562	blood:
2	chr12:104442014..104443659-chr12:104530642..104533573,2	MCF-7	breast:
3	chr12:104441752..104444274-chr12:104682358..104684016,2	K562	blood:
4	chr12:104440302..104444353-chr12:104456677..104458918,3	K562	blood:
5	chr12:104441740..104444353-chr12:104456837..104458918,2	K562	blood:

Variant related genes	Relation type
ENSG00000198431	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000111727	Chromatin interaction
ENSG00000120820	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11111878	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs15805	0.80[CHB][hapmap]
rs1843371	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1920410	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1920411	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1920412	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2220210	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4423256	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7961041	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[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	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17035146	SLC25A3	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104439400-104443400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:104439400-104443400	Weak transcription	Left Ventricle	heart
3	chr12:104439400-104443400	Weak transcription	Lung	lung
4	chr12:104439400-104443400	Weak transcription	Right Ventricle	heart
5	chr12:104439400-104443800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr12:104439600-104443400	Weak transcription	Psoas Muscle	Psoas
7	chr12:104440000-104443400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:104440200-104443000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:104440200-104443200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:104441800-104444600	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr12:104442000-104443000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:104442000-104443000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:104442000-104443000	Enhancers	Adipose Nuclei	Adipose
14	chr12:104442000-104443600	Active TSS	Fetal Muscle Trunk	muscle
15	chr12:104442000-104444400	Active TSS	Aorta	Aorta
16	chr12:104442400-104443000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
17	chr12:104442400-104443000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:104442400-104443000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:104442400-104443000	Flanking Active TSS	NHDF-Ad	bronchial
20	chr12:104442400-104443200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:104442400-104443200	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr12:104442400-104443200	Weak transcription	A549	lung
23	chr12:104442400-104443200	Flanking Active TSS	HMEC	breast
24	chr12:104442400-104443200	Flanking Active TSS	NH-A	brain
25	chr12:104442400-104443400	Flanking Active TSS	Osteobl	bone
26	chr12:104442400-104444400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
27	chr12:104442400-104444600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:104442600-104443000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
29	chr12:104442600-104443000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:104442600-104443000	Flanking Active TSS	Hela-S3	cervix
31	chr12:104442600-104443200	Active TSS	Fetal Intestine Small	intestine
32	chr12:104442600-104443200	Enhancers	Placenta Amnion	Placenta Amnion
33	chr12:104442600-104443400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:104442600-104444600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr12:104442600-104444600	Active TSS	Right Atrium	heart
36	chr12:104442800-104443000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:104442800-104443000	Flanking Active TSS	Fetal Lung	lung
38	chr12:104442800-104443000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr12:104442800-104443400	Active TSS	Duodenum Mucosa	Duodenum
40	chr12:104442800-104443400	Active TSS	Fetal Muscle Leg	muscle
41	chr12:104442800-104443400	Enhancers	NHEK	skin
42	chr12:104442800-104443600	Active TSS	HSMMtube	muscle
43	chr12:104442800-104443800	Active TSS	HSMM	muscle
44	chr12:104442800-104444000	Active TSS	Fetal Stomach	stomach
45	chr12:104442800-104444000	Active TSS	Rectal Smooth Muscle	rectum
46	chr12:104442800-104444000	Active TSS	NHLF	lung
47	chr12:104442800-104444200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:104442800-104444200	Active TSS	Colon Smooth Muscle	Colon
49	chr12:104442800-104444200	Active TSS	Stomach Smooth Muscle	stomach
50	chr12:104442800-104444400	Active TSS	Ovary	ovary

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