Variant report

Variant	rs10875712
Chromosome Location	chr12:48363253-48363254
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48362502..48365466-chr12:48366201..48368271,2	K562	blood:
2	chr12:48362584..48365917-chr12:48368904..48372045,3	K562	blood:
3	chr12:48360838..48363620-chr12:48364578..48367184,3	K562	blood:
4	chr12:48360987..48363483-chr12:48393695..48396604,4	MCF-7	breast:
5	chr12:48356037..48360072-chr12:48360475..48364952,9	K562	blood:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction
ENSG00000134291	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11168325	0.90[YRI][hapmap]
rs11609253	0.80[MEX][hapmap]
rs2286024	0.82[MEX][hapmap];0.85[TSI][hapmap]
rs4760607	1.00[CHB][hapmap]
rs4760674	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap]
rs7307880	0.82[MEX][hapmap];0.89[TSI][hapmap]
rs7964582	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv519174	chr12:48359984-48365265	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv899061	chr12:48360620-48389023	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10875712	AQP6	cis	parietal	SCAN
rs10875712	TMEM106C	cis	multi-tissue	Pritchard
rs10875712	VDR	cis	parietal	SCAN
rs10875712	NCKAP5L	cis	cerebellum	SCAN
rs10875712	C12orf68	cis	parietal	SCAN
rs10875712	DNAJC22	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48358200-48364200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:48358200-48366200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:48358200-48366200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:48358400-48364600	Weak transcription	Ovary	ovary
5	chr12:48358400-48365000	Weak transcription	Osteobl	bone
6	chr12:48358400-48365200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:48358400-48366400	Weak transcription	Fetal Brain Male	brain
8	chr12:48358400-48367800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:48358400-48367800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:48358400-48369800	Weak transcription	Brain Angular Gyrus	brain
11	chr12:48358400-48373000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:48358600-48363400	Strong transcription	Fetal Thymus	thymus
13	chr12:48358600-48363600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:48358600-48363800	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:48358600-48365200	Weak transcription	HSMMtube	muscle
16	chr12:48358600-48366600	Weak transcription	Fetal Lung	lung
17	chr12:48358600-48369400	Weak transcription	Fetal Kidney	kidney
18	chr12:48358600-48381400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:48358800-48366000	Weak transcription	HepG2	liver
20	chr12:48358800-48366200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:48359000-48364000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:48359200-48363400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:48359200-48364000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:48359200-48364400	Strong transcription	Stomach Smooth Muscle	stomach
25	chr12:48359200-48364600	Strong transcription	Placenta	Placenta
26	chr12:48359200-48364800	Strong transcription	Primary T cells from cord blood	blood
27	chr12:48359200-48384000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:48359400-48363400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:48359600-48363400	Genic enhancers	Fetal Muscle Leg	muscle
30	chr12:48359600-48363600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:48359600-48363800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr12:48359600-48366600	Strong transcription	Thymus	Thymus
33	chr12:48359800-48363400	Strong transcription	Gastric	stomach
34	chr12:48359800-48363400	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr12:48359800-48364400	Weak transcription	HSMM	muscle
36	chr12:48360000-48363400	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:48360000-48363400	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:48360000-48364600	Weak transcription	Right Ventricle	heart
39	chr12:48360000-48366000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:48360000-48368200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr12:48360200-48363400	Strong transcription	Fetal Intestine Large	intestine
42	chr12:48360200-48363400	Strong transcription	Dnd41	blood
43	chr12:48360200-48369600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:48360400-48364600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:48360600-48363400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr12:48360600-48363400	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr12:48360800-48363400	Strong transcription	Aorta	Aorta
48	chr12:48360800-48363400	Strong transcription	Pancreas	Pancrea
49	chr12:48361000-48363400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:48361000-48363400	Strong transcription	Liver	Liver

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