Variant report

Variant	rs7978685
Chromosome Location	chr12:57103154-57103155
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57082048..57083806-chr12:57102806..57104517,2	MCF-7	breast:
2	chr12:57088163..57090039-chr12:57103030..57105439,2	MCF-7	breast:
3	chr12:57080452..57082852-chr12:57101909..57106660,4	K562	blood:
4	chr12:57101910..57104991-chr12:57106569..57110622,4	MCF-7	breast:
5	chr12:57080452..57082981-chr12:57101571..57103409,2	K562	blood:
6	chr12:57098550..57104951-chr12:57116953..57119967,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110958	Chromatin interaction
ENSG00000196531	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1026565	0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10450	0.83[TSI][hapmap]
rs10459246	0.81[ASN][1000 genomes]
rs10747770	0.88[ASN][1000 genomes]
rs10783796	0.96[ASN][1000 genomes]
rs10876914	0.81[AMR][1000 genomes]
rs10876915	0.81[AMR][1000 genomes]
rs10876916	0.93[CHB][hapmap]
rs10876918	0.93[ASN][1000 genomes]
rs1107479	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs11171914	0.92[CHB][hapmap]
rs11171917	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11171951	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs11171956	0.95[ASN][1000 genomes]
rs11171986	0.85[JPT][hapmap];0.88[MEX][hapmap]
rs1131514	0.93[ASN][1000 genomes]
rs11837319	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12227117	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12229457	0.93[CHB][hapmap]
rs12828563	0.97[ASN][1000 genomes]
rs1465081	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1466382	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1563896	0.87[CHB][hapmap]
rs1975875	0.93[ASN][1000 genomes]
rs1979325	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2035081	0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2035082	0.96[ASN][1000 genomes]
rs2255074	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs2290893	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs2290894	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2926741	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2926743	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2926747	0.92[ASN][1000 genomes]
rs2926748	0.96[ASN][1000 genomes]
rs2950387	0.80[CHB][hapmap]
rs2950390	0.93[CHB][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap]
rs2958123	0.93[CHB][hapmap]
rs2958127	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2958130	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2958132	0.93[ASN][1000 genomes]
rs2958134	0.86[ASN][1000 genomes]
rs2958139	0.93[TSI][hapmap]
rs2958145	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2958148	0.94[ASN][1000 genomes]
rs2958149	1.00[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2958153	1.00[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2958154	0.93[CHB][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap]
rs2958155	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs3214051	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4277148	0.85[JPT][hapmap]
rs4759254	0.81[CHB][hapmap]
rs4759256	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4788	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902	0.96[ASN][1000 genomes]
rs67046307	0.81[AMR][1000 genomes]
rs7137749	0.89[ASN][1000 genomes]
rs7295862	0.80[ASN][1000 genomes]
rs7309526	0.82[AMR][1000 genomes]
rs7313074	1.00[ASW][hapmap];0.94[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];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7315472	0.81[AMR][1000 genomes]
rs7966391	0.90[ASN][1000 genomes]
rs7967600	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7980317	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7980378	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs898609	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs898611	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs941207	0.86[CHB][hapmap]
rs9634246	1.00[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]

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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv559016	chr12:57095815-57112637	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7978685	KRT1	cis	cerebellum	SCAN
rs7978685	PRIM1	cis	parietal	SCAN
rs7978685	GPR182	cis	parietal	SCAN
rs7978685	CELA1	cis	cerebellum	SCAN
rs7978685	HSD17B6	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57083800-57105200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr12:57089000-57109600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:57090400-57104600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:57090400-57104800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:57093400-57104800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:57094800-57104800	Weak transcription	NH-A	brain
7	chr12:57094800-57105000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr12:57095000-57104600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:57095000-57104800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:57095000-57104800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:57095000-57104800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:57095000-57104800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:57095000-57104800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:57095000-57104800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr12:57095000-57104800	Weak transcription	Osteobl	bone
16	chr12:57095000-57105000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:57095000-57105000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:57095000-57105000	Weak transcription	Primary B cells from cord blood	blood
19	chr12:57095000-57105200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:57095200-57105000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:57095400-57104800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:57095400-57104800	Weak transcription	Placenta	Placenta
23	chr12:57099800-57104800	Weak transcription	A549	lung
24	chr12:57100000-57105200	Weak transcription	Thymus	Thymus
25	chr12:57100400-57104800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:57100400-57105200	Weak transcription	GM12878-XiMat	blood
27	chr12:57100400-57106600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr12:57100600-57104800	Weak transcription	NHEK	skin
29	chr12:57100600-57105200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:57100800-57105000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:57100800-57105000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:57100800-57105000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:57100800-57105000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:57101200-57105000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr12:57101400-57106200	Weak transcription	K562	blood
36	chr12:57101600-57104800	Weak transcription	Fetal Muscle Leg	muscle
37	chr12:57101600-57105200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:57101800-57105200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr12:57101800-57106400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:57102000-57104800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr12:57102000-57104800	Weak transcription	HSMM	muscle
42	chr12:57102200-57104800	Weak transcription	Liver	Liver
43	chr12:57102400-57103600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr12:57102400-57104600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr12:57102400-57106400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:57102600-57104600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:57102600-57105000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr12:57102600-57105000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:57102600-57105200	Weak transcription	HSMMtube	muscle
50	chr12:57102600-57105400	Weak transcription	Fetal Intestine Small	intestine

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