Variant report

Variant	rs7954619
Chromosome Location	chr12:56209976-56209977
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56208283-56210944	K562	blood:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56208117..56217611-chr12:56318345..56328982,45	MCF-7	breast:
2	chr12:56135540..56139368-chr12:56208041..56213329,11	MCF-7	breast:
3	chr12:56209321..56212347-chr12:56235221..56238369,3	K562	blood:
4	chr12:56122056..56124298-chr12:56209901..56211592,3	MCF-7	breast:
5	chr12:56142466..56145089-chr12:56208136..56210341,2	K562	blood:
6	chr12:56208204..56214844-chr12:56359426..56363484,9	MCF-7	breast:
7	chr12:56209766..56212313-chr12:56351329..56354004,2	MCF-7	breast:
8	chr12:56196551..56198632-chr12:56208205..56210492,2	K562	blood:
9	chr12:56209485..56211287-chr12:56328988..56331281,2	MCF-7	breast:
10	chr12:56209755..56212447-chr12:56551879..56553739,2	MCF-7	breast:
11	chr12:56208546..56216914-chr12:56318326..56328671,24	MCF-7	breast:
12	chr12:56209486..56213209-chr12:56366653..56370251,5	MCF-7	breast:
13	chr12:56149836..56151992-chr12:56207924..56210313,2	MCF-7	breast:
14	chr12:56209786..56211523-chr12:56320983..56323005,2	K562	blood:
15	chr12:56208394..56211844-chr12:56510539..56512389,3	MCF-7	breast:
16	chr12:54672412..54674185-chr12:56208193..56211080,2	MCF-7	breast:
17	chr12:56121599..56124065-chr12:56209598..56212420,4	MCF-7	breast:
18	chr12:56207854..56211065-chr12:56313696..56316486,3	MCF-7	breast:
19	chr12:56209963..56212805-chr12:56473917..56475602,2	MCF-7	breast:
20	chr12:56208453..56210322-chr12:56434019..56436970,2	K562	blood:

No data

Variant related genes	Relation type
ORMDL2	TF binding region
ENSG00000185664	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000135486	Chromatin interaction
ENSG00000123342	Chromatin interaction
ENSG00000258554	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000094916	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000123374	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1081732	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10876851	1.00[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876852	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10876854	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11171681	0.91[CHB][hapmap]
rs11829536	0.90[JPT][hapmap]
rs12372076	0.92[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1681087	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291268	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2694012	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2887998	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7305787	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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs772262	0.93[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs772263	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7954839	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7965333	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7954619	RDH5	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56183400-56210600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:56195600-56210600	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:56195800-56210200	Weak transcription	Aorta	Aorta
4	chr12:56203400-56210600	Weak transcription	Esophagus	oesophagus
5	chr12:56203400-56210600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:56205200-56210000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
7	chr12:56206400-56210200	Weak transcription	Right Atrium	heart
8	chr12:56206400-56210800	Weak transcription	Gastric	stomach
9	chr12:56207600-56210000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:56207800-56210000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:56207800-56210600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr12:56208000-56210400	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr12:56208200-56210400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:56208400-56210200	Enhancers	Liver	Liver
15	chr12:56208400-56210600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:56208600-56210200	Weak transcription	Right Ventricle	heart
17	chr12:56208600-56210600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:56208600-56210600	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr12:56208800-56210200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:56208800-56210600	Enhancers	Brain Cingulate Gyrus	brain
21	chr12:56209000-56210000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:56209000-56210000	Genic enhancers	Primary hematopoietic stem cells	blood
23	chr12:56209000-56210000	Genic enhancers	Fetal Lung	lung
24	chr12:56209000-56210000	Genic enhancers	Placenta Amnion	Placenta Amnion
25	chr12:56209200-56210000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
26	chr12:56209200-56210000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:56209200-56210000	Genic enhancers	Brain Anterior Caudate	brain
28	chr12:56209200-56210000	Transcr. at gene 5' and 3'	HUVEC	blood vessel
29	chr12:56209200-56210200	Enhancers	Primary B cells from cord blood	blood
30	chr12:56209200-56210200	Transcr. at gene 5' and 3'	Hela-S3	cervix
31	chr12:56209200-56210400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:56209200-56210600	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr12:56209200-56210600	Enhancers	Colonic Mucosa	Colon
34	chr12:56209200-56210600	Enhancers	Stomach Mucosa	stomach
35	chr12:56209400-56210000	Flanking Active TSS	GM12878-XiMat	blood
36	chr12:56209400-56210200	Enhancers	Brain Angular Gyrus	brain
37	chr12:56209400-56210200	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr12:56209400-56210200	Enhancers	Rectal Smooth Muscle	rectum
39	chr12:56209400-56210400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:56209400-56210600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:56209400-56212200	Active TSS	Fetal Brain Female	brain
42	chr12:56209400-56212400	Active TSS	NHLF	lung
43	chr12:56209600-56210000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:56209600-56210000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr12:56209600-56210000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:56209600-56210000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:56209600-56210000	Enhancers	Fetal Kidney	kidney
48	chr12:56209600-56210000	Enhancers	HSMMtube	muscle
49	chr12:56209600-56210200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr12:56209600-56210200	Active TSS	HUES6 Cell Line	embryonic stem cell

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