Variant report

Variant	rs12422312
Chromosome Location	chr12:12347909-12347910
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	chr12:12347779..12350511-chr12:12354038..12356966,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070018	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10466849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845488	0.87[CEU][hapmap]
rs10845499	1.00[CHB][hapmap]
rs11054720	1.00[CHB][hapmap]
rs11054729	1.00[CHB][hapmap]
rs11054732	1.00[CHB][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap]
rs11054765	1.00[CHB][hapmap]
rs11834671	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299540	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313200	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs12317629	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12320259	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs12321417	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425946	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56087862	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488506	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs718403	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs7301012	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs7308022	0.81[ASW][hapmap];1.00[CHB][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap]
rs74061128	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061156	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061161	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957531	1.00[CHB][hapmap]
rs7963810	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs7973718	1.00[CHB][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap]
rs7978064	1.00[CHB][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12422312	RIMKLB	cis	cerebellum	SCAN
rs12422312	LRP6	cis	parietal	SCAN
rs12422312	OR51E2	trans	cerebellum	SCAN

Chromatin state (count:74 , 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	chr12:12334400-12348400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:12334400-12349200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:12334400-12349600	Weak transcription	Dnd41	blood
11	chr12:12334400-12351200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:12334400-12352000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:12334400-12354000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr12:12334400-12367600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr12:12334600-12349200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:12334800-12352800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:12335200-12352000	Weak transcription	HSMM	muscle
18	chr12:12335200-12365800	Weak transcription	NHEK	skin
19	chr12:12335800-12354000	Weak transcription	HSMMtube	muscle
20	chr12:12336000-12352000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:12336000-12354200	Weak transcription	Primary T cells from cord blood	blood
22	chr12:12336000-12355600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr12:12336200-12360000	Weak transcription	Aorta	Aorta
24	chr12:12336200-12363200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr12:12336200-12369800	Weak transcription	Left Ventricle	heart
26	chr12:12336200-12381000	Weak transcription	Pancreas	Pancrea
27	chr12:12336400-12348800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:12336400-12349600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:12336400-12357400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:12337600-12348200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:12337800-12348400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:12338200-12349000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:12338200-12355800	Weak transcription	Stomach Mucosa	stomach
34	chr12:12339000-12350800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:12339200-12357600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:12339800-12350600	Weak transcription	Fetal Intestine Small	intestine
37	chr12:12339800-12350600	Weak transcription	Fetal Stomach	stomach
38	chr12:12340000-12348600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:12340200-12349600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr12:12340600-12349600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:12340600-12359400	Weak transcription	Ovary	ovary
42	chr12:12340800-12349600	Weak transcription	Liver	Liver
43	chr12:12342200-12360000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr12:12344000-12349000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:12344000-12349600	Weak transcription	HMEC	breast
46	chr12:12344000-12355200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:12344000-12367800	Weak transcription	NHLF	lung
48	chr12:12344200-12348000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:12344200-12348200	Weak transcription	HUVEC	blood vessel
50	chr12:12344200-12349800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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