Variant report

Variant	rs774211
Chromosome Location	chr12:56920939-56920940
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56919517..56922316-chr12:56981865..56983826,2	K562	blood:
2	chr12:56918887..56922105-chr12:57038272..57040603,3	MCF-7	breast:
3	chr12:56916521..56918137-chr12:56919957..56922129,2	MCF-7	breast:
4	chr12:56920527..56922162-chr12:56923065..56925052,2	K562	blood:

Variant related genes	Relation type
ENSG00000207031	Chromatin interaction
ENSG00000110955	Chromatin interaction
ENSG00000201579	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1043011	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs12232026	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2638287	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2638301	0.89[AMR][1000 genomes]
rs2638315	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs2657879	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs2657880	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs2657896	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2657907	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2694917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2694919	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2933235	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3759091	0.82[CHB][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap]
rs7302925	0.82[JPT][hapmap]
rs7304944	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs774213	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs774215	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs799260	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs799261	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs813497	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][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	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv899106	chr12:56905558-57004668	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs774211	SPRYD4	cis	lymphoblastoid	seeQTL
rs774211	STAC3	cis	parietal	SCAN
rs774211	ITGA5	cis	cerebellum	SCAN
rs774211	ORMDL2	cis	parietal	SCAN
rs774211	SPRYD4	Cis_1M	lymphoblastoid	RTeQTL
rs774211	RBMS2	cis	lymphoblastoid	seeQTL
rs774211	DCD	cis	parietal	SCAN
rs774211	SPRYD4	cis	multi-tissue	Pritchard

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56916600-56923200	Weak transcription	Small Intestine	intestine
2	chr12:56916800-56930400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:56917000-56921600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:56917000-56923000	Weak transcription	Aorta	Aorta
5	chr12:56917000-56958000	Weak transcription	Ovary	ovary
6	chr12:56917200-56923000	Weak transcription	Psoas Muscle	Psoas
7	chr12:56917200-56956200	Weak transcription	Primary T cells from cord blood	blood
8	chr12:56917200-56959200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:56917400-56924600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:56917400-56931400	Weak transcription	Right Ventricle	heart
11	chr12:56918000-56921400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:56918600-56930000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr12:56919400-56921600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:56919400-56929600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:56919600-56923200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:56919600-56924200	Weak transcription	Spleen	Spleen
17	chr12:56920000-56921000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr12:56920000-56921000	Weak transcription	Lung	lung
19	chr12:56920000-56921400	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr12:56920200-56921000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr12:56920200-56921000	Flanking Active TSS	HMEC	breast
22	chr12:56920200-56921000	Flanking Active TSS	Osteobl	bone
23	chr12:56920200-56921200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr12:56920200-56921200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:56920200-56921200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:56920200-56921200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr12:56920200-56921200	Flanking Active TSS	HUVEC	blood vessel
28	chr12:56920200-56921200	Flanking Active TSS	NH-A	brain
29	chr12:56920200-56921400	Enhancers	Fetal Stomach	stomach
30	chr12:56920200-56921600	Enhancers	HepG2	liver
31	chr12:56920200-56922000	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr12:56920200-56922000	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr12:56920200-56922000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:56920400-56921000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:56920400-56921000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:56920400-56921000	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr12:56920400-56921000	Enhancers	Duodenum Mucosa	Duodenum
38	chr12:56920400-56921200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:56920400-56921200	Flanking Active TSS	Hela-S3	cervix
40	chr12:56920400-56921200	Flanking Active TSS	HSMMtube	muscle
41	chr12:56920600-56921000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr12:56920600-56921000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr12:56920600-56921000	Flanking Active TSS	Colon Smooth Muscle	Colon
44	chr12:56920600-56921000	Flanking Active TSS	Fetal Heart	heart
45	chr12:56920600-56921000	Flanking Active TSS	NHDF-Ad	bronchial
46	chr12:56920600-56921200	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr12:56920600-56921200	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr12:56920600-56921400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:56920600-56921400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:56920600-56921800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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