Variant report

Variant	rs7959622
Chromosome Location	chr12:56107691-56107692
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	FOSL2	chr12:56107569-56107870	A549	lung:	n/a	n/a
2	GATA3	chr12:56107413-56108015	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr12:56107488-56107986	U87	brain:	n/a	n/a
4	NFIC	chr12:56107533-56107952	SK-N-SH	brain:	n/a	n/a
5	MYC	chr12:56107617-56107705	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr12:56107523-56107877	MCF10A-Er-Src	breast:	n/a	chr12:56107628-56107637 chr12:56107629-56107638
7	JUND	chr12:56107063-56107938	SK-N-SH	brain:	n/a	chr12:56107755-56107766
8	STAT3	chr12:56107522-56107717	MCF10A-Er-Src	breast:	n/a	chr12:56107628-56107637 chr12:56107629-56107638
9	FOS	chr12:56107490-56107904	MCF10A-Er-Src	breast:	n/a	n/a
10	PBX3	chr12:56107359-56107997	SK-N-SH	brain:	n/a	n/a
11	JUND	chr12:56107423-56108068	SK-N-SH	brain:	n/a	chr12:56107755-56107766
12	JUN	chr12:56107570-56107878	HepG2	liver:	n/a	chr12:56107729-56107742
13	CEBPB	chr12:56107501-56107878	Hela-S3	cervix:	n/a	n/a
14	E2F4	chr12:56107547-56107750	MCF10A-Er-Src	breast:	n/a	chr12:56107734-56107743 chr12:56107732-56107741
15	STAT3	chr12:56107433-56107907	MCF10A-Er-Src	breast:	n/a	chr12:56107628-56107637 chr12:56107629-56107638
16	BRCA1	chr12:56107554-56107812	Hela-S3	cervix:	n/a	n/a
17	FOSL2	chr12:56107452-56107871	SK-N-SH	brain:	n/a	n/a
18	PBX3	chr12:56107380-56107962	SK-N-SH	brain:	n/a	n/a
19	STAT3	chr12:56107492-56107877	MCF10A-Er-Src	breast:	n/a	chr12:56107628-56107637 chr12:56107629-56107638
20	JUN	chr12:56107453-56107850	Hela-S3	cervix:	n/a	chr12:56107729-56107742
21	FOSL2	chr12:56107323-56107924	SK-N-SH	brain:	n/a	n/a
22	FOS	chr12:56107522-56107890	MCF10A-Er-Src	breast:	n/a	n/a
23	FOS	chr12:56107420-56107940	MCF10A-Er-Src	breast:	n/a	n/a
24	JUND	chr12:56107406-56107907	SK-N-SH	brain:	n/a	chr12:56107755-56107766
25	JUND	chr12:56107549-56107896	HepG2	liver:	n/a	chr12:56107755-56107766
26	FOS	chr12:56107443-56107933	MCF10A-Er-Src	breast:	n/a	n/a
27	MAFK	chr12:56107556-56107833	Hela-S3	cervix:	n/a	n/a
28	JUND	chr12:56107478-56107893	Hela-S3	cervix:	n/a	chr12:56107755-56107766
29	MAFK	chr12:56107450-56107836	IMR90	lung:	n/a	n/a
30	TCF12	chr12:56107445-56108011	SK-N-SH	brain:	n/a	n/a
31	MYC	chr12:56107523-56107877	MCF10A-Er-Src	breast:	n/a	n/a
32	RCOR1	chr12:56106522-56108070	IMR90	lung:	n/a	n/a
33	CEBPB	chr12:56107507-56107884	IMR90	lung:	n/a	n/a
34	POLR2A	chr12:56107554-56107872	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56107674..56111560-chr12:56417665..56420637,3	MCF-7	breast:
2	chr12:56098605..56104708-chr12:56107025..56111403,7	MCF-7	breast:
3	chr12:56105036..56107744-chr12:56108446..56111418,3	MCF-7	breast:
4	chr12:56107652..56112121-chr12:56134921..56139203,6	MCF-7	breast:

Variant related genes	Relation type
BLOC1S1	TF binding region
ENSG00000258311	TF binding region
ITGA7	TF binding region
ENSG00000135424	Chromatin interaction
ENSG00000258311	Chromatin interaction
ENSG00000135441	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000123411	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12308277	1.00[GIH][hapmap]
rs13193	0.89[EUR][1000 genomes]
rs1463591	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs17118032	1.00[GIH][hapmap]
rs2231462	1.00[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs2231464	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4457792	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58599597	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948625	chr12:55838718-56118833	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv525231	chr12:56076919-56124332	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
4	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7959622	RDH5	cis	lymphoblastoid	seeQTL
rs7959622	RDH5	cis	multi-tissue	Pritchard
rs7959622	BLOC1S1	cis	lymphoblastoid	seeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56102600-56109000	Weak transcription	Brain Angular Gyrus	brain
2	chr12:56102600-56109200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:56102800-56107800	Enhancers	Colon Smooth Muscle	Colon
4	chr12:56102800-56107800	Active TSS	Right Atrium	heart
5	chr12:56102800-56107800	Active TSS	Right Ventricle	heart
6	chr12:56102800-56109000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:56102800-56109200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:56102800-56109200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:56102800-56109200	Weak transcription	Spleen	Spleen
10	chr12:56103600-56109400	Weak transcription	Lung	lung
11	chr12:56103800-56109000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:56105400-56108000	Enhancers	Rectal Smooth Muscle	rectum
13	chr12:56105600-56107800	Enhancers	HSMMtube	muscle
14	chr12:56105600-56108000	Enhancers	Muscle Satellite Cultured Cells	--
15	chr12:56105600-56108000	Enhancers	HSMM	muscle
16	chr12:56105800-56107800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr12:56105800-56108000	Enhancers	NH-A	brain
18	chr12:56106200-56108200	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr12:56106600-56108000	Enhancers	Osteobl	bone
20	chr12:56106800-56108200	Enhancers	Hela-S3	cervix
21	chr12:56106800-56109200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr12:56106800-56109400	Weak transcription	Aorta	Aorta
23	chr12:56107000-56109000	Weak transcription	Liver	Liver
24	chr12:56107000-56109000	Weak transcription	Brain Anterior Caudate	brain
25	chr12:56107000-56109000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr12:56107000-56109200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:56107000-56109200	Weak transcription	Brain Substantia Nigra	brain
28	chr12:56107000-56109200	Weak transcription	K562	blood
29	chr12:56107200-56108800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr12:56107200-56108800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr12:56107200-56108800	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:56107200-56109000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:56107200-56109000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:56107200-56109000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr12:56107200-56109000	Weak transcription	Fetal Lung	lung
36	chr12:56107200-56109200	Weak transcription	Fetal Stomach	stomach
37	chr12:56107200-56109400	Weak transcription	Psoas Muscle	Psoas
38	chr12:56107400-56107800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:56107400-56107800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:56107400-56107800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:56107400-56107800	Enhancers	Fetal Heart	heart
42	chr12:56107400-56107800	Enhancers	A549	lung
43	chr12:56107400-56108000	Enhancers	NHEK	skin
44	chr12:56107400-56108200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:56107400-56108800	Weak transcription	NHLF	lung
46	chr12:56107400-56109000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr12:56107400-56109200	Weak transcription	Left Ventricle	heart
48	chr12:56107600-56107800	Enhancers	Brain Hippocampus Middle	brain
49	chr12:56107600-56107800	Enhancers	HMEC	breast
50	chr12:56107600-56108000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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