Variant report

Variant	rs775306
Chromosome Location	chr12:67664578-67664579
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr12:67663842-67664623	K562	blood:	n/a	n/a
2	ZNF384	chr12:67664187-67664729	GM12878	blood:	n/a	n/a
3	E2F4	chr12:67664002-67664706	MCF10A-Er-Src	breast:	n/a	chr12:67664188-67664195 chr12:67664187-67664196 chr12:67664509-67664521 chr12:67664187-67664199 chr12:67664188-67664195 chr12:67664510-67664517 chr12:67664510-67664517 chr12:67664188-67664195 chr12:67664187-67664195 chr12:67664510-67664517
4	HCFC1	chr12:67661643-67665072	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr12:67661895-67664635	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:67662044-67665627	K562	blood:	n/a	n/a
7	CHD1	chr12:67662085-67664765	GM12878	blood:	n/a	chr12:67662928-67662937 chr12:67663750-67663760

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:67664539..67666217-chr12:67712484..67714487,2	K562	blood:
2	chr12:67460777..67464522-chr12:67661841..67665703,9	MCF-7	breast:

Variant related genes	Relation type
GGTA2P	TF binding region
ENSG00000256248	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10506544	0.90[ASN][1000 genomes]
rs1060350	0.97[ASN][1000 genomes]
rs1066389	0.97[ASN][1000 genomes]
rs1066390	0.97[ASN][1000 genomes]
rs1066391	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1066396	0.97[ASN][1000 genomes]
rs1066398	0.97[ASN][1000 genomes]
rs1066399	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1066404	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10784619	0.99[ASN][1000 genomes]
rs10784624	0.81[ASN][1000 genomes]
rs1082700	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1082710	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10878596	0.98[ASN][1000 genomes]
rs10878601	0.87[ASN][1000 genomes]
rs1092600	0.97[ASN][1000 genomes]
rs1112445	0.90[ASN][1000 genomes]
rs11176647	0.94[ASN][1000 genomes]
rs11176657	0.95[ASN][1000 genomes]
rs11176677	0.97[ASN][1000 genomes]
rs11176683	0.97[ASN][1000 genomes]
rs11176690	0.92[ASN][1000 genomes]
rs11176695	0.90[ASN][1000 genomes]
rs11176700	0.87[ASN][1000 genomes]
rs1136080	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1137465	0.97[ASN][1000 genomes]
rs1143954	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1143956	0.98[ASN][1000 genomes]
rs1144939	0.93[ASN][1000 genomes]
rs1152877	0.97[ASN][1000 genomes]
rs1152895	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1152896	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1152897	1.00[ASN][1000 genomes]
rs1152898	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1152901	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1152902	1.00[ASN][1000 genomes]
rs1161085	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1161087	0.87[ASN][1000 genomes]
rs1161089	0.97[ASN][1000 genomes]
rs1161090	0.97[ASN][1000 genomes]
rs1161092	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1183126	0.93[ASN][1000 genomes]
rs1184743	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1185918	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12366819	0.97[ASN][1000 genomes]
rs12369715	0.90[ASN][1000 genomes]
rs12370954	0.96[ASN][1000 genomes]
rs12422358	0.90[ASN][1000 genomes]
rs12422968	0.97[ASN][1000 genomes]
rs12424158	1.00[ASN][1000 genomes]
rs1252364	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252386	0.90[ASN][1000 genomes]
rs1252387	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1252388	0.90[ASN][1000 genomes]
rs1252402	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252405	1.00[ASN][1000 genomes]
rs1252407	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1252419	0.98[ASN][1000 genomes]
rs1252422	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252424	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12580790	1.00[ASN][1000 genomes]
rs1272089	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1392587	0.98[ASN][1000 genomes]
rs1500431	0.92[ASN][1000 genomes]
rs1583648	0.92[ASN][1000 genomes]
rs1612693	0.91[ASN][1000 genomes]
rs1697232	0.97[ASN][1000 genomes]
rs1697233	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17781745	0.93[ASN][1000 genomes]
rs1921000	0.87[ASN][1000 genomes]
rs2028213	0.97[ASN][1000 genomes]
rs2091698	0.96[ASN][1000 genomes]
rs2118311	0.92[ASN][1000 genomes]
rs2178466	0.82[ASN][1000 genomes]
rs2248751	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2438109	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2576941	0.98[ASN][1000 genomes]
rs3861890	0.98[ASN][1000 genomes]
rs4913538	0.98[ASN][1000 genomes]
rs4913540	0.97[ASN][1000 genomes]
rs4913541	0.92[ASN][1000 genomes]
rs61918267	0.97[ASN][1000 genomes]
rs61920672	1.00[ASN][1000 genomes]
rs698123	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs710626	0.99[ASN][1000 genomes]
rs710627	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs710628	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs710629	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs710630	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs710800	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7134743	0.90[ASN][1000 genomes]
rs775309	0.98[ASN][1000 genomes]
rs775312	0.98[ASN][1000 genomes]
rs775644	0.92[ASN][1000 genomes]
rs775645	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs775651	0.87[ASN][1000 genomes]
rs775652	0.87[ASN][1000 genomes]
rs775655	0.87[ASN][1000 genomes]
rs775660	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs796522	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7968645	1.00[ASN][1000 genomes]
rs7973565	0.99[ASN][1000 genomes]
rs7977430	0.97[ASN][1000 genomes]
rs811820	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs811827	1.00[ASN][1000 genomes]
rs814290	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541524	chr12:67311057-67700349	Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1054111	chr12:67556780-67865542	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs775306	CAND1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67661600-67665000	Active TSS	K562	blood
2	chr12:67661600-67665200	Active TSS	GM12878-XiMat	blood
3	chr12:67661800-67664600	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr12:67661800-67664600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr12:67661800-67664800	Active TSS	Aorta	Aorta
6	chr12:67661800-67664800	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr12:67661800-67664800	Active TSS	Stomach Mucosa	stomach
8	chr12:67661800-67665000	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr12:67661800-67665000	Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr12:67661800-67665000	Active TSS	Brain Angular Gyrus	brain
11	chr12:67661800-67665000	Active TSS	Fetal Kidney	kidney
12	chr12:67661800-67665000	Active TSS	Right Atrium	heart
13	chr12:67661800-67665000	Active TSS	Thymus	Thymus
14	chr12:67661800-67665000	Active TSS	A549	lung
15	chr12:67661800-67665000	Active TSS	HSMM	muscle
16	chr12:67661800-67665200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:67661800-67665200	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr12:67661800-67665200	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr12:67661800-67665200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:67661800-67665200	Active TSS	Psoas Muscle	Psoas
21	chr12:67661800-67665400	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr12:67661800-67665400	Active TSS	H1 Cell Line	embryonic stem cell
23	chr12:67661800-67665400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:67661800-67665600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:67661800-67666000	Active TSS	NHLF	lung
26	chr12:67662000-67664600	Active TSS	Fetal Muscle Trunk	muscle
27	chr12:67662000-67664800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr12:67662000-67664800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:67662000-67665000	Active TSS	H9 Cell Line	embryonic stem cell
30	chr12:67662000-67665200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr12:67662000-67665200	Active TSS	Ovary	ovary
32	chr12:67662000-67665200	Active TSS	Right Ventricle	heart
33	chr12:67662000-67665400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:67662000-67665600	Active TSS	NHDF-Ad	bronchial
35	chr12:67662200-67664600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:67662200-67664600	Active TSS	Brain Anterior Caudate	brain
37	chr12:67662200-67664600	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr12:67662200-67664600	Active TSS	Colon Smooth Muscle	Colon
39	chr12:67662200-67664600	Active TSS	NHEK	skin
40	chr12:67662200-67664800	Active TSS	Hela-S3	cervix
41	chr12:67662200-67665000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:67662200-67665000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:67662200-67665000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:67662200-67665000	Active TSS	Fetal Brain Female	brain
45	chr12:67662200-67665000	Active TSS	Osteobl	bone
46	chr12:67662200-67665200	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr12:67662200-67665400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:67662200-67665400	Active TSS	HSMMtube	muscle
49	chr12:67662200-67665600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr12:67662200-67666200	Active TSS	iPS-20b Cell Line	embryonic stem cell

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