Variant report

Variant	rs10861302
Chromosome Location	chr12:105383976-105383977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105376961..105378683-chr12:105383835..105385377,2	K562	blood:
2	chr12:105379993..105381811-chr12:105382055..105386132,5	K562	blood:
3	chr12:105378619..105382506-chr12:105382781..105387261,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151131	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10778361	0.98[ASN][1000 genomes]
rs10778363	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10861299	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10861301	0.97[ASN][1000 genomes]
rs10861303	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861304	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861308	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10861309	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10861310	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10861311	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10861313	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap]
rs11112263	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11112272	0.81[CEU][hapmap]
rs11112274	0.83[CEU][hapmap]
rs11112284	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs11112286	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112287	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112288	0.85[CEU][hapmap]
rs11112296	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112297	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112299	0.99[ASN][1000 genomes]
rs11112306	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1129593	0.91[CHB][hapmap]
rs12581510	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12581542	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16890	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17036612	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4075503	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4281549	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4318051	1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs4331189	0.81[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4473015	0.99[ASN][1000 genomes]
rs6539176	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7134342	0.99[ASN][1000 genomes]
rs7297572	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7302931	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304326	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7307234	0.84[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7308025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7308266	0.97[ASN][1000 genomes]
rs7308568	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7308574	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7309375	0.98[ASN][1000 genomes]
rs7311995	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73387268	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7958263	0.98[ASN][1000 genomes]
rs7970173	0.97[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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv869	chr12:105363425-105394904	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription 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	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10861302	MGC40397	cis	multi-tissue	Pritchard
rs10861302	C12orf45	cis	Lymphoblastoid	GTEx
rs10861302	C12orf45	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105380800-105386000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:105380800-105386200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:105380800-105386200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:105380800-105386400	Weak transcription	Esophagus	oesophagus
5	chr12:105381000-105384000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:105381000-105386000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:105381000-105386800	Weak transcription	Psoas Muscle	Psoas
8	chr12:105381000-105388600	Weak transcription	Right Ventricle	heart
9	chr12:105381200-105384800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:105381400-105385000	Weak transcription	Fetal Heart	heart
11	chr12:105381400-105385600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:105381400-105385600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:105381400-105386000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:105381600-105384200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:105381600-105384200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr12:105381600-105384600	Weak transcription	Fetal Stomach	stomach
17	chr12:105381600-105384800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr12:105381600-105384800	Weak transcription	Brain Anterior Caudate	brain
19	chr12:105381600-105385000	Weak transcription	Placenta	Placenta
20	chr12:105381600-105385400	Weak transcription	NHDF-Ad	bronchial
21	chr12:105381600-105385800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:105381600-105385800	Weak transcription	NHLF	lung
23	chr12:105381600-105386000	Weak transcription	Colonic Mucosa	Colon
24	chr12:105381600-105386200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr12:105381600-105386400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr12:105381600-105387000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr12:105381600-105388600	Weak transcription	Spleen	Spleen
28	chr12:105381600-105392400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:105381600-105392400	Weak transcription	Stomach Mucosa	stomach
30	chr12:105381800-105384400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:105381800-105384600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:105381800-105384600	Weak transcription	Pancreas	Pancrea
33	chr12:105381800-105384800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:105381800-105384800	Weak transcription	Brain Substantia Nigra	brain
35	chr12:105381800-105384800	Weak transcription	Fetal Intestine Small	intestine
36	chr12:105381800-105385200	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:105381800-105385600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:105381800-105385800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr12:105381800-105385800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr12:105381800-105385800	Weak transcription	NH-A	brain
41	chr12:105381800-105386000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr12:105381800-105386200	Weak transcription	Thymus	Thymus
43	chr12:105381800-105386800	Weak transcription	Fetal Brain Male	brain
44	chr12:105381800-105388200	Weak transcription	HSMMtube	muscle
45	chr12:105381800-105388400	Weak transcription	Aorta	Aorta
46	chr12:105381800-105388400	Weak transcription	Brain Germinal Matrix	brain
47	chr12:105381800-105389200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr12:105381800-105392400	Weak transcription	Right Atrium	heart
49	chr12:105381800-105392800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr12:105381800-105392800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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