Variant report

Variant	rs10778341
Chromosome Location	chr12:104989818-104989819
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	chr12:104989262..104996194-chr12:104996249..105001190,9	K562	blood:
2	chr12:104985616..104988878-chr12:104989745..104992186,3	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10861239	1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10861240	0.93[EUR][1000 genomes]
rs10861241	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861242	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861243	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861245	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861246	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10861248	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112118	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11112119	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11112120	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11112121	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11112122	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11112123	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112124	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112125	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112126	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11112127	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11610583	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1529423	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1529424	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17035902	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1704898	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17813400	1.00[CEU][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4964824	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4964825	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs61938575	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6539161	0.94[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7301126	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7301450	0.92[EUR][1000 genomes]
rs7306538	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7306664	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73187418	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73187426	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73187427	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73187429	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7954025	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7954312	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7979531	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1035364	chr12:104948307-105003705	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10778341	C12orf42	cis	cerebellum	SCAN
rs10778341	POLR3B	cis	parietal	SCAN
rs10778341	SPIC	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104971000-104990600	Weak transcription	Lung	lung
2	chr12:104973800-104990800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:104974600-104990600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:104975600-104992000	Weak transcription	Gastric	stomach
5	chr12:104976800-104996800	Weak transcription	Primary T cells from cord blood	blood
6	chr12:104980200-104997600	Weak transcription	Esophagus	oesophagus
7	chr12:104980600-104990600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:104982600-104994800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:104982800-104995400	Weak transcription	Thymus	Thymus
10	chr12:104983200-104996800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr12:104983200-104997800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:104985000-104996400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:104986200-104990200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr12:104986200-104990600	Weak transcription	HMEC	breast
15	chr12:104986400-104992000	Enhancers	K562	blood
16	chr12:104987000-104990800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:104987000-104992400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:104987200-104992800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:104987600-104992600	Weak transcription	Spleen	Spleen
20	chr12:104987800-104990000	Enhancers	Primary T cells fromperipheralblood	blood
21	chr12:104987800-104997800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:104988000-104990000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:104988000-104997000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr12:104988000-104997200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr12:104988400-104990400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr12:104988400-104990600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr12:104988600-104994800	Enhancers	Primary B cells from peripheral blood	blood
28	chr12:104988800-104990000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:104988800-104993000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:104988800-104995600	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr12:104988800-104995600	Enhancers	GM12878-XiMat	blood
32	chr12:104989000-104991600	Enhancers	A549	lung
33	chr12:104989200-104990000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:104989200-104990000	Enhancers	NHDF-Ad	bronchial
35	chr12:104989200-104990000	Enhancers	Osteobl	bone
36	chr12:104989200-104990200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:104989200-104990200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:104989200-104990200	Enhancers	NH-A	brain
39	chr12:104989200-104991000	Enhancers	NHEK	skin
40	chr12:104989200-104991400	Enhancers	Fetal Stomach	stomach
41	chr12:104989200-104991600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:104989200-104991600	Enhancers	HSMM	muscle
43	chr12:104989200-104991800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:104989200-104992800	Enhancers	Fetal Thymus	thymus
45	chr12:104989200-104997800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:104989400-104990000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:104989400-104990000	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr12:104989400-104990000	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr12:104989400-104990200	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr12:104989400-104990200	Enhancers	Right Atrium	heart

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