Variant report

Variant	rs12617696
Chromosome Location	chr2:153012130-153012131
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	chr2:152893310..152893909-chr2:153011664..153012216,2	MCF-7	breast:
2	chr2:153010671..153012696-chr2:153030750..153032348,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115145	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10178907	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10184862	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10200655	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10803946	0.81[MEX][hapmap]
rs10930916	0.82[CHB][hapmap]
rs10930958	0.86[CHB][hapmap];0.94[CHD][hapmap]
rs11693948	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12612031	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12617139	0.86[CHB][hapmap]
rs17398329	0.86[CHB][hapmap]
rs2345639	0.86[CHB][hapmap]
rs3768650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3820702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4664079	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4664082	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4664531	0.91[CEU][hapmap];0.88[TSI][hapmap]
rs4664534	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4664536	1.00[CHD][hapmap]
rs6650771	0.86[CHB][hapmap]
rs6738680	0.86[CHB][hapmap]
rs6740224	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7369093	0.88[AMR][1000 genomes]
rs7603232	0.86[CHB][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv1847028	chr2:152863856-153045036	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1004308	chr2:152980087-153154534	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535985	chr2:152980087-153154534	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv459740	chr2:152986041-153045036	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv583316	chr2:152986041-153045036	Bivalent/Poised TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	esv3693434	chr2:152998467-153208713	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12617696	STAM2	cis	parietal	SCAN
rs12617696	STAM2	cis	multi-tissue	Pritchard

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152974200-153017000	Weak transcription	Colonic Mucosa	Colon
2	chr2:152976000-153014800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:152976200-153013400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:152976400-153013400	Weak transcription	Brain Angular Gyrus	brain
5	chr2:152978200-153021400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:152981800-153024800	Weak transcription	Brain Substantia Nigra	brain
7	chr2:152982400-153013400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:152983800-153013400	Weak transcription	Psoas Muscle	Psoas
9	chr2:152991800-153018400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:152996200-153013400	Weak transcription	Right Ventricle	heart
11	chr2:152998400-153013200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:152998400-153013400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:153000200-153031000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:153001800-153013600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:153001800-153013600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:153002200-153013400	Weak transcription	Aorta	Aorta
17	chr2:153002200-153023600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr2:153002400-153022000	Weak transcription	Lung	lung
19	chr2:153002800-153030400	Weak transcription	Thymus	Thymus
20	chr2:153003200-153013400	Weak transcription	Left Ventricle	heart
21	chr2:153003200-153013600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:153003200-153028400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:153003600-153013400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr2:153003600-153013400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:153003600-153013800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:153003600-153014000	Weak transcription	Ovary	ovary
27	chr2:153003600-153028000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:153003800-153013400	Weak transcription	Brain Anterior Caudate	brain
29	chr2:153003800-153013600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:153004000-153018400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:153004000-153022400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr2:153004200-153013200	Weak transcription	Fetal Intestine Large	intestine
33	chr2:153004200-153013600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:153004200-153013600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr2:153004200-153013600	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:153004200-153013800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:153004200-153023800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:153004400-153013600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:153004400-153013600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:153004400-153016400	Weak transcription	NH-A	brain
41	chr2:153004400-153023600	Weak transcription	HSMM	muscle
42	chr2:153004400-153023600	Weak transcription	NHDF-Ad	bronchial
43	chr2:153004600-153013800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:153004600-153014000	Weak transcription	Dnd41	blood
45	chr2:153004600-153021200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:153004800-153013600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr2:153004800-153013600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:153004800-153015000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr2:153004800-153022400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:153005200-153013600	Weak transcription	Fetal Lung	lung

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