Variant report

Variant	rs2724610
Chromosome Location	chr12:11846366-11846367
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	chr12:11800032..11801851-chr12:11845652..11848182,2	MCF-7	breast:

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2724651	0.85[CEU][hapmap];0.88[MEX][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2724652	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2724653	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2724657	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3020923	0.88[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7959282	0.88[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes]

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	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2724610	CLEC7A	cis	cerebellum	SCAN
rs2724610	GPRC5A	cis	parietal	SCAN
rs2724610	FOXJ2	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11815000-11850600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:11822000-11850000	Weak transcription	HMEC	breast
3	chr12:11822200-11851000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:11826000-11851200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:11827400-11879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:11827800-11851800	Weak transcription	Ovary	ovary
7	chr12:11831000-11848600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:11831200-11847200	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:11831600-11852600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:11832600-11848200	Weak transcription	HSMMtube	muscle
11	chr12:11835600-11847000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:11837200-11858600	Weak transcription	Fetal Intestine Large	intestine
13	chr12:11838000-11850000	Weak transcription	HUVEC	blood vessel
14	chr12:11838000-11850400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr12:11838000-11858000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:11838200-11846600	Weak transcription	Esophagus	oesophagus
17	chr12:11838200-11848200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:11838400-11848000	Weak transcription	Primary B cells from cord blood	blood
19	chr12:11838400-11848000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr12:11838400-11854200	Weak transcription	Fetal Heart	heart
21	chr12:11838600-11848000	Weak transcription	NH-A	brain
22	chr12:11838800-11872200	Weak transcription	Primary T cells from cord blood	blood
23	chr12:11839200-11857800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:11839400-11853400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:11839400-11859000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr12:11840800-11846800	Strong transcription	GM12878-XiMat	blood
27	chr12:11840800-11854400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr12:11840800-11859200	Weak transcription	Fetal Kidney	kidney
29	chr12:11841200-11846600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:11841200-11854200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:11841200-11856800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr12:11841600-11846400	Weak transcription	Spleen	Spleen
33	chr12:11841600-11847800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr12:11841600-11848200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:11841600-11853600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:11841800-11846400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:11841800-11846400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr12:11841800-11846400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:11841800-11848200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:11841800-11848200	Weak transcription	Gastric	stomach
41	chr12:11841800-11853600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:11841800-11853800	Weak transcription	Small Intestine	intestine
43	chr12:11841800-11854200	Weak transcription	Fetal Lung	lung
44	chr12:11841800-11854200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:11841800-11860200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr12:11841800-11867400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:11842000-11848000	Weak transcription	Stomach Mucosa	stomach
48	chr12:11842400-11847800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:11842400-11848000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:11842400-11854200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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