Variant report

Variant	rs1072778
Chromosome Location	chr12:31824971-31824972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:149223795..149225326-chr12:31823553..31825073,2	MCF-7	breast:
2	chr12:31812744..31814749-chr12:31824204..31825895,2	MCF-7	breast:
3	chr12:31819291..31822149-chr12:31822447..31825439,3	K562	blood:
4	chr12:31820306..31823293-chr12:31823300..31825334,2	K562	blood:
5	chr1:149223762..149224509-chr12:31824553..31825553,4	HCT-116	colon:

Variant related genes	Relation type
ENSG00000206737	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10743763	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771864	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10843994	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10843998	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11051539	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11051553	0.87[EUR][1000 genomes]
rs1115971	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12303424	0.87[CEU][hapmap]
rs12316119	0.92[ASN][1000 genomes]
rs12818390	0.92[CEU][hapmap]
rs12819673	0.86[EUR][1000 genomes]
rs2200232	0.91[ASN][1000 genomes]
rs2374171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2388926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4272863	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap]
rs4931537	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7295568	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73090337	0.94[ASN][1000 genomes]
rs73090387	0.89[EUR][1000 genomes]
rs7309916	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7953032	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7957042	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7966525	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7968792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7970095	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7971803	0.85[EUR][1000 genomes]
rs7980264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs900609	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs900610	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers 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 target site	41 gene(s)	inside rSNPs	diseases
4	esv3432694	chr12:31801467-32109828	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv898966	chr12:31810126-31944985	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1072778	REP15	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31813000-31826000	Weak transcription	Gastric	stomach
2	chr12:31813200-31837000	Weak transcription	Fetal Brain Male	brain
3	chr12:31813400-31825200	Weak transcription	Aorta	Aorta
4	chr12:31813400-31825400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:31813400-31825600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:31813400-31826600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr12:31813400-31835200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:31813400-31835600	Weak transcription	Brain Angular Gyrus	brain
9	chr12:31813400-31836200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:31815200-31840600	Weak transcription	Pancreas	Pancrea
11	chr12:31815800-31826200	Weak transcription	Brain Substantia Nigra	brain
12	chr12:31817400-31850400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:31822400-31825000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr12:31822400-31827200	Weak transcription	Fetal Stomach	stomach
15	chr12:31822400-31828600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:31822400-31835600	Weak transcription	Fetal Lung	lung
17	chr12:31822400-31836600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:31822400-31840600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:31822600-31825600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:31822600-31826000	Weak transcription	Left Ventricle	heart
21	chr12:31822600-31826200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:31822600-31826200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:31822600-31827800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:31822600-31828000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:31822600-31829600	Weak transcription	Brain Hippocampus Middle	brain
26	chr12:31822600-31830400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:31822600-31830800	Weak transcription	HSMMtube	muscle
28	chr12:31822600-31835200	Weak transcription	Ovary	ovary
29	chr12:31822600-31835600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:31822600-31835600	Weak transcription	Fetal Brain Female	brain
31	chr12:31822600-31835600	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:31822600-31836000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:31822600-31836400	Weak transcription	Brain Anterior Caudate	brain
34	chr12:31822600-31862000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr12:31822600-31874200	Weak transcription	Right Ventricle	heart
36	chr12:31822800-31826400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr12:31822800-31826600	Weak transcription	HSMM	muscle
38	chr12:31822800-31826800	Weak transcription	Placenta	Placenta
39	chr12:31822800-31827200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:31822800-31828800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr12:31822800-31830400	Weak transcription	A549	lung
42	chr12:31822800-31830600	Weak transcription	Brain Germinal Matrix	brain
43	chr12:31822800-31830800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:31822800-31834800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr12:31822800-31835000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:31822800-31835400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:31822800-31835600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr12:31822800-31835600	Weak transcription	Dnd41	blood
49	chr12:31823000-31825400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:31823000-31835400	Weak transcription	Fetal Intestine Small	intestine

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