Variant report

Variant	rs7295568
Chromosome Location	chr12:31867856-31867857
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:31811076..31814149-chr12:31866420..31869336,3	K562	blood:
2	chr12:31867508..31869786-chr12:31900848..31903323,2	K562	blood:
3	chr12:31810792..31812576-chr12:31866206..31867920,2	K562	blood:
4	chr12:31866804..31870237-chr12:31900678..31903673,4	K562	blood:

Variant related genes	Relation type
ENSG00000256843	Chromatin interaction
ENSG00000139160	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1072778	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]
rs10743763	0.90[CHB][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10771864	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10843994	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs10843998	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11051539	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11051553	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1115971	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12303424	0.87[CEU][hapmap]
rs12316119	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12818390	0.92[CEU][hapmap]
rs12819673	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2200232	0.91[ASN][1000 genomes]
rs2374171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2388926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4272863	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs73090337	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73090387	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7309916	0.88[ASN][1000 genomes]
rs7953032	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7957042	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7966525	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs7968792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7970095	0.93[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7971803	0.83[EUR][1000 genomes]
rs7980264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs900609	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs900610	0.93[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];0.94[MKK][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
6	nsv898967	chr12:31858031-31899475	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv2422415	chr12:31863360-31930722	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv558100	chr12:31866833-32185924	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7295568	REP15	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31822600-31874200	Weak transcription	Right Ventricle	heart
2	chr12:31827000-31871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:31838600-31881000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:31839800-31871800	Weak transcription	Gastric	stomach
5	chr12:31841600-31870000	Weak transcription	Pancreas	Pancrea
6	chr12:31844600-31871800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:31846400-31871800	Weak transcription	Lung	lung
8	chr12:31849000-31880000	Weak transcription	Psoas Muscle	Psoas
9	chr12:31851000-31880800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:31852800-31871000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:31852800-31879600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:31859000-31871800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:31860400-31872400	Weak transcription	Fetal Kidney	kidney
14	chr12:31860600-31874000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:31860800-31871800	Weak transcription	Ovary	ovary
16	chr12:31860800-31881000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:31861000-31871800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:31862200-31880600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:31862400-31871800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:31862600-31868000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:31862600-31868200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr12:31862600-31868400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:31862600-31871200	Weak transcription	Fetal Lung	lung
24	chr12:31862600-31871800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:31862800-31871800	Weak transcription	Aorta	Aorta
26	chr12:31862800-31874200	Weak transcription	Left Ventricle	heart
27	chr12:31863800-31868000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr12:31864000-31871800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:31864800-31868200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:31865200-31868400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr12:31865400-31871800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:31866600-31868400	Weak transcription	Fetal Thymus	thymus
33	chr12:31866600-31871600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:31867200-31868200	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr12:31867200-31868800	Enhancers	Brain Anterior Caudate	brain
36	chr12:31867200-31868800	Enhancers	Placenta	Placenta
37	chr12:31867400-31868000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:31867400-31868000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:31867400-31868400	Enhancers	Primary B cells from peripheral blood	blood
40	chr12:31867400-31868400	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr12:31867400-31868400	Enhancers	Placenta Amnion	Placenta Amnion
42	chr12:31867400-31868600	Enhancers	Brain Cingulate Gyrus	brain
43	chr12:31867600-31868000	Enhancers	Brain Hippocampus Middle	brain
44	chr12:31867600-31868200	Enhancers	Primary hematopoietic stem cells	blood
45	chr12:31867600-31868400	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr12:31867600-31868600	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr12:31867600-31868600	Enhancers	A549	lung
48	chr12:31867600-31868800	Enhancers	Brain Substantia Nigra	brain
49	chr12:31867600-31868800	Enhancers	Stomach Mucosa	stomach
50	chr12:31867600-31868800	Enhancers	Thymus	Thymus

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