Variant report

Variant	rs879732
Chromosome Location	chr12:12240199-12240200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12238838..12240368-chr12:12419597..12421163,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070018	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1615942	0.86[GIH][hapmap]
rs2111166	0.89[GIH][hapmap];0.87[LWK][hapmap]
rs2160523	0.87[GIH][hapmap];0.87[LWK][hapmap];0.80[MEX][hapmap]
rs2448051	0.82[GIH][hapmap]

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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv975623	chr12:12238184-12243964	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv557583	chr12:12238317-12253591	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs879732	CLEC12A	cis	parietal	SCAN
rs879732	HIST4H4	cis	cerebellum	SCAN
rs879732	MGP	cis	parietal	SCAN
rs879732	ZNF705A	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12225000-12255000	Weak transcription	Small Intestine	intestine
2	chr12:12225800-12240200	Weak transcription	Fetal Stomach	stomach
3	chr12:12226600-12245000	Weak transcription	Fetal Brain Male	brain
4	chr12:12232800-12257000	Weak transcription	HSMMtube	muscle
5	chr12:12234800-12259600	Weak transcription	Aorta	Aorta
6	chr12:12235200-12242000	Weak transcription	NHLF	lung
7	chr12:12235400-12243600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:12235400-12244600	Weak transcription	Colonic Mucosa	Colon
9	chr12:12235400-12245000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:12235400-12245200	Weak transcription	Pancreas	Pancrea
11	chr12:12235400-12260200	Weak transcription	Gastric	stomach
12	chr12:12235400-12260800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr12:12235400-12278800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:12235600-12240800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr12:12237400-12259800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:12238000-12245000	Strong transcription	Duodenum Mucosa	Duodenum
17	chr12:12238400-12240200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:12238400-12241000	Enhancers	H9 Cell Line	embryonic stem cell
19	chr12:12238400-12241000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:12238600-12241200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr12:12238600-12241800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:12238600-12242000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:12238800-12240200	Weak transcription	Fetal Intestine Large	intestine
24	chr12:12239000-12240200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr12:12239000-12241200	Enhancers	H1 Cell Line	embryonic stem cell
26	chr12:12239200-12240600	Enhancers	Brain Germinal Matrix	brain
27	chr12:12239200-12241000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:12239200-12241000	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr12:12239200-12241200	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr12:12239200-12241200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr12:12239200-12241800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr12:12239400-12241000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:12239400-12241200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr12:12239400-12241800	Enhancers	HepG2	liver
35	chr12:12239600-12240600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:12239600-12240800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:12239600-12240800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:12239600-12240800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr12:12239600-12241000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:12239600-12241400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:12239600-12249200	Strong transcription	Fetal Intestine Small	intestine
42	chr12:12239800-12240400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr12:12239800-12240400	Enhancers	Brain Cingulate Gyrus	brain
44	chr12:12239800-12240800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:12239800-12241000	Enhancers	Brain Anterior Caudate	brain
46	chr12:12240000-12240400	Enhancers	Fetal Lung	lung
47	chr12:12240000-12240400	Enhancers	Stomach Mucosa	stomach
48	chr12:12240000-12241000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:12240000-12242000	Strong transcription	Rectal Mucosa Donor 31	rectum

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