Variant report

Variant	rs2417086
Chromosome Location	chr12:12350113-12350114
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	chr12:12347779..12350511-chr12:12354038..12356966,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070018	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10431302	0.85[ASW][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap]
rs10492120	0.90[CHB][hapmap]
rs10743980	0.90[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs10772536	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10772537	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10772540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10772542	0.90[CHB][hapmap];0.86[CHD][hapmap]
rs10772547	0.90[CHB][hapmap]
rs10845489	0.93[CEU][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10845491	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10845492	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10845494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845495	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845501	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11054718	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11054721	1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11054724	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11054731	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11054744	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11609634	0.93[CEU][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12366664	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12823243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17819999	0.92[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1819871	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2284396	0.93[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.81[EUR][1000 genomes]
rs2302684	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2417085	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3782528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4477532	0.93[CEU][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4763785	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61920859	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6488507	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7294695	0.93[CEU][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7302808	0.81[EUR][1000 genomes]
rs7305037	0.96[CEU][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7956548	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7956971	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7966410	0.92[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7973531	0.90[CHB][hapmap]
rs7979447	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv832332	chr12:12344027-12484966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2417086	AICDA	cis	parietal	SCAN
rs2417086	FAM90A1	cis	cerebellum	SCAN
rs2417086	LRP6	cis	parietal	SCAN
rs2417086	CLEC2A	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12304000-12353000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:12312000-12350600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:12312200-12355800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:12312200-12362000	Weak transcription	Hela-S3	cervix
5	chr12:12315400-12371600	Weak transcription	Lung	lung
6	chr12:12325400-12360000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:12334200-12350800	Weak transcription	Fetal Thymus	thymus
8	chr12:12334400-12351200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:12334400-12352000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:12334400-12354000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:12334400-12367600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr12:12334800-12352800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:12335200-12352000	Weak transcription	HSMM	muscle
14	chr12:12335200-12365800	Weak transcription	NHEK	skin
15	chr12:12335800-12354000	Weak transcription	HSMMtube	muscle
16	chr12:12336000-12352000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr12:12336000-12354200	Weak transcription	Primary T cells from cord blood	blood
18	chr12:12336000-12355600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:12336200-12360000	Weak transcription	Aorta	Aorta
20	chr12:12336200-12363200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr12:12336200-12369800	Weak transcription	Left Ventricle	heart
22	chr12:12336200-12381000	Weak transcription	Pancreas	Pancrea
23	chr12:12336400-12357400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:12338200-12355800	Weak transcription	Stomach Mucosa	stomach
25	chr12:12339000-12350800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:12339200-12357600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:12339800-12350600	Weak transcription	Fetal Intestine Small	intestine
28	chr12:12339800-12350600	Weak transcription	Fetal Stomach	stomach
29	chr12:12340600-12359400	Weak transcription	Ovary	ovary
30	chr12:12342200-12360000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:12344000-12355200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:12344000-12367800	Weak transcription	NHLF	lung
33	chr12:12344200-12351400	Weak transcription	Fetal Intestine Large	intestine
34	chr12:12344200-12352000	Weak transcription	Brain Anterior Caudate	brain
35	chr12:12344200-12353000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:12344200-12353200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:12344200-12353400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:12344200-12354000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:12344200-12355400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:12344200-12367200	Weak transcription	Colon Smooth Muscle	Colon
41	chr12:12344200-12367400	Weak transcription	Brain Substantia Nigra	brain
42	chr12:12344200-12367800	Weak transcription	NH-A	brain
43	chr12:12344200-12377000	Weak transcription	NHDF-Ad	bronchial
44	chr12:12344400-12353000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:12344400-12353200	Weak transcription	Fetal Heart	heart
46	chr12:12344400-12354200	Weak transcription	K562	blood
47	chr12:12345600-12353000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:12346400-12353400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:12347200-12352000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:12347400-12355200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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