Variant report

Variant	rs10861239
Chromosome Location	chr12:104979240-104979241
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104976850..104978699-chr12:104978951..104981176,2	K562	blood:
2	chr12:104974220..104976063-chr12:104977911..104980754,2	MCF-7	breast:
3	chr12:104973001..104975710-chr12:104978478..104980869,2	K562	blood:
4	chr12:104978478..104980060-chr12:104982412..104984027,2	K562	blood:

Variant related genes	Relation type
ENSG00000171310	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10778341	1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10861240	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861241	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10861242	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10861243	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10861244	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10861245	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10861246	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10861248	1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11112118	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11112119	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11112120	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11112121	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11112122	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11112123	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11112124	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11112125	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11112126	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11112127	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11610583	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1529423	1.00[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1529424	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17035902	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17813400	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61938575	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6539161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7301126	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7301450	0.90[EUR][1000 genomes]
rs7306538	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7306664	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73187418	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73187426	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73187427	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73187429	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7954025	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7954312	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7979531	0.98[AMR][1000 genomes];0.94[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10861239	C12orf42	cis	cerebellum	SCAN
rs10861239	SPIC	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104965400-104982200	Weak transcription	Left Ventricle	heart
2	chr12:104971000-104990600	Weak transcription	Lung	lung
3	chr12:104971400-104979400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:104971600-104982200	Weak transcription	Right Atrium	heart
5	chr12:104972200-104989800	Weak transcription	Fetal Brain Male	brain
6	chr12:104973400-104979800	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:104973600-104979400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:104973800-104990800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:104974000-104982000	Weak transcription	NH-A	brain
10	chr12:104974200-104981800	Weak transcription	NHDF-Ad	bronchial
11	chr12:104974200-104981800	Weak transcription	Osteobl	bone
12	chr12:104974400-104979600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:104974400-104984800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:104974600-104987600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr12:104974600-104988800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr12:104974600-104990600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:104975000-104982200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:104975000-104988800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr12:104975600-104988400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:104975600-104992000	Weak transcription	Gastric	stomach
21	chr12:104976000-104987800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:104976200-104979800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:104976600-104980000	Strong transcription	Dnd41	blood
24	chr12:104976800-104996800	Weak transcription	Primary T cells from cord blood	blood
25	chr12:104977000-104980400	Weak transcription	Fetal Kidney	kidney
26	chr12:104977200-104979800	Weak transcription	A549	lung
27	chr12:104977200-104982200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr12:104977200-104987200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr12:104977400-104979400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:104977400-104979800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr12:104977400-104980200	Weak transcription	K562	blood
32	chr12:104977400-104982200	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr12:104977800-104979600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:104977800-104980000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:104977800-104982200	Weak transcription	Thymus	Thymus
36	chr12:104978000-104980600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr12:104978000-104989600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr12:104978400-104989600	Weak transcription	Primary B cells from cord blood	blood
39	chr12:104978600-104979600	Strong transcription	Primary hematopoietic stem cells	blood
40	chr12:104978600-104979600	Genic enhancers	GM12878-XiMat	blood
41	chr12:104978600-104982200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr12:104978800-104980200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:104978800-104981200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:104978800-104981800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:104979000-104979400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:104979000-104980000	Weak transcription	Fetal Brain Female	brain
47	chr12:104979000-104980200	Genic enhancers	Fetal Thymus	thymus
48	chr12:104979000-104986000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:104979200-104979800	Enhancers	NHEK	skin
50	chr12:104979200-104980000	Genic enhancers	Primary B cells from peripheral blood	blood

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