Variant report

Variant	rs4298967
Chromosome Location	chr12:2408194-2408195
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	chr12:2404999..2406703-chr12:2407924..2410819,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1006737	0.92[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs1024582	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744560	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10774035	0.92[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10774036	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10774037	1.00[CHB][hapmap];0.81[MEX][hapmap]
rs11062157	1.00[JPT][hapmap]
rs11062170	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12311439	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12315711	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2159100	0.92[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs4765905	0.92[CEU][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs4765913	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs4765914	1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[MEX][hapmap]
rs758170	0.92[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs769087	0.92[CEU][hapmap];0.82[EUR][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	nsv1040370	chr12:2021395-2671017	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv948400	chr12:2022411-2601363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4298967	CACNA1C	cis	cerebellum	SCAN
rs4298967	EFCAB4B	cis	parietal	SCAN
rs4298967	SLC6A12	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2393800-2409000	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr12:2394000-2412200	Weak transcription	Colonic Mucosa	Colon
3	chr12:2398400-2415000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:2398400-2415200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr12:2398600-2410200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr12:2399600-2413400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:2401000-2410800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:2402400-2409800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:2402800-2410200	Weak transcription	Aorta	Aorta
10	chr12:2403400-2408600	Enhancers	Primary B cells from cord blood	blood
11	chr12:2403400-2408600	Enhancers	Right Atrium	heart
12	chr12:2403400-2408800	Enhancers	Left Ventricle	heart
13	chr12:2403400-2409200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:2403600-2409000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:2403600-2409000	Enhancers	Fetal Thymus	thymus
16	chr12:2403800-2408800	Enhancers	Primary hematopoietic stem cells	blood
17	chr12:2403800-2409000	Enhancers	Thymus	Thymus
18	chr12:2404200-2410000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:2404200-2415400	Weak transcription	Esophagus	oesophagus
20	chr12:2404600-2408200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr12:2405200-2410800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:2405200-2411400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr12:2405400-2408200	Weak transcription	Fetal Kidney	kidney
24	chr12:2405400-2408400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:2405400-2410600	Weak transcription	Fetal Lung	lung
26	chr12:2405400-2414600	Weak transcription	Fetal Brain Male	brain
27	chr12:2405600-2408400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:2405600-2410200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:2405600-2410200	Weak transcription	Fetal Stomach	stomach
30	chr12:2405600-2410200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:2405600-2415000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:2405800-2408400	Weak transcription	Osteobl	bone
33	chr12:2405800-2409800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:2405800-2410000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:2405800-2410800	Weak transcription	Spleen	Spleen
36	chr12:2405800-2417600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr12:2406000-2408400	Weak transcription	NHLF	lung
38	chr12:2406000-2408600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:2406000-2410000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:2406000-2410600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr12:2406400-2409600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:2406400-2410000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:2406400-2411400	Weak transcription	Brain Hippocampus Middle	brain
44	chr12:2406400-2411400	Weak transcription	Lung	lung
45	chr12:2406600-2408600	Weak transcription	NHDF-Ad	bronchial
46	chr12:2406600-2410200	Weak transcription	HSMMtube	muscle
47	chr12:2406600-2420600	Weak transcription	Brain Germinal Matrix	brain
48	chr12:2406800-2410000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:2406800-2411400	Weak transcription	Brain Angular Gyrus	brain
50	chr12:2407000-2408800	Enhancers	Fetal Heart	heart

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