Variant report

Variant	rs2460967
Chromosome Location	chr8:119627892-119627893
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	chr8:119626648..119628226-chr8:119632877..119634473,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177570	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10108302	0.84[ASN][1000 genomes]
rs1568484	0.96[ASN][1000 genomes]
rs2460964	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2460965	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460966	0.93[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2460968	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460970	0.93[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2460971	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2460972	0.93[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2460975	0.85[ASN][1000 genomes]
rs2460976	0.85[ASN][1000 genomes]
rs2460979	0.85[ASN][1000 genomes]
rs2460982	0.82[ASN][1000 genomes]
rs2460983	0.84[ASN][1000 genomes]
rs2514576	0.82[ASN][1000 genomes]
rs2514591	0.92[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs2514592	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2514593	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2514594	0.86[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2514596	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2514600	0.85[ASN][1000 genomes]
rs2514608	0.85[ASN][1000 genomes]
rs2514609	0.85[ASN][1000 genomes]
rs2514610	0.85[ASN][1000 genomes]
rs2514611	0.82[ASN][1000 genomes]
rs2514612	0.82[ASN][1000 genomes]
rs3133404	0.87[ASN][1000 genomes]
rs62531943	0.89[ASN][1000 genomes]
rs880033	0.93[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs880034	0.86[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891413	chr8:119607281-119679668	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv1814789	chr8:119627671-119672134	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv465786	chr8:119627671-119767165	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv612048	chr8:119627671-119767165	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2460967	SAMD12	cis	multi-tissue	Pritchard
rs2460967		cis	Lymphoblastoid	GTEx
rs2460967	Hs.453941	cis	multi-tissue	Pritchard
rs2460967	LOC377696	cis	multi-tissue	Pritchard
rs2460967	SAMD12	cis	Lymphoblastoid	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:119605800-119631800	Weak transcription	Fetal Intestine Small	intestine
2	chr8:119609200-119633000	Weak transcription	Gastric	stomach
3	chr8:119609400-119633600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr8:119619400-119632200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr8:119623200-119632200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr8:119623800-119632800	Weak transcription	Fetal Lung	lung
7	chr8:119624200-119632800	Weak transcription	Pancreas	Pancrea
8	chr8:119624400-119628600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr8:119625200-119632000	Weak transcription	Fetal Intestine Large	intestine
10	chr8:119626400-119628200	Enhancers	HSMMtube	muscle
11	chr8:119626400-119630600	Enhancers	Brain Angular Gyrus	brain
12	chr8:119626600-119628000	Enhancers	Esophagus	oesophagus
13	chr8:119626600-119628000	Enhancers	Lung	lung
14	chr8:119626600-119628200	Enhancers	HSMM	muscle
15	chr8:119626600-119629000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr8:119626600-119629000	Enhancers	Brain Anterior Caudate	brain
17	chr8:119626600-119630600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr8:119626800-119630800	Enhancers	Brain Hippocampus Middle	brain
19	chr8:119627000-119628000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr8:119627000-119628800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr8:119627000-119632000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr8:119627000-119632200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr8:119627000-119632400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr8:119627200-119628000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr8:119627200-119628000	Weak transcription	Right Ventricle	heart
26	chr8:119627200-119633200	Weak transcription	Aorta	Aorta
27	chr8:119627400-119628000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr8:119627400-119628600	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr8:119627400-119628600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr8:119627600-119628600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr8:119627600-119629200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr8:119627600-119630600	Enhancers	Brain Substantia Nigra	brain
33	chr8:119627600-119632800	Weak transcription	NHEK	skin
34	chr8:119627600-119633600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr8:119627800-119628200	Flanking Active TSS	NH-A	brain
36	chr8:119627800-119630000	Enhancers	Brain Cingulate Gyrus	brain
37	chr8:119627800-119632000	Weak transcription	GM12878-XiMat	blood
38	chr8:119627800-119632400	Weak transcription	Left Ventricle	heart
39	chr8:119627800-119632400	Weak transcription	Right Atrium	heart
40	chr8:119627800-119632800	Weak transcription	Colonic Mucosa	Colon
41	chr8:119627800-119632800	Weak transcription	Spleen	Spleen

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