Variant report

Variant	rs12774228
Chromosome Location	chr10:5977275-5977276
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5971270..5973563-chr10:5974618..5977378,2	K562	blood:
2	chr10:5973930..5977726-chr10:5979603..5983323,6	K562	blood:
3	chr10:5973085..5975782-chr10:5976092..5977796,2	K562	blood:
4	chr10:5964443..5967389-chr10:5974579..5977579,3	K562	blood:
5	chr10:5965483..5967118-chr10:5975794..5977895,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134452	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10508298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255698	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255774	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255780	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255971	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255974	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256009	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359234	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12360409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12767690	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12777477	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12781700	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12785055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17319759	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];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976655	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985072	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2387092	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];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36049919	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3891620	0.84[LWK][hapmap];0.95[YRI][hapmap]
rs56369297	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61832959	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6602330	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7067928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082434	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090411	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7893735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7919913	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1041261	chr10:5962635-6052196	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1050983	chr10:5963921-6052196	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12774228	AKR1C3	cis	parietal	SCAN
rs12774228	IL15RA	cis	parietal	SCAN
rs12774228	AKR1C2	cis	cerebellum	SCAN
rs12774228	ANKRD16	cis	cerebellum	SCAN
rs12774228	ANKRD16	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5944000-5981600	Strong transcription	Fetal Intestine Small	intestine
2	chr10:5944600-5981200	Strong transcription	Fetal Thymus	thymus
3	chr10:5945800-5980800	Strong transcription	Thymus	Thymus
4	chr10:5947000-5980800	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr10:5947000-5981600	Strong transcription	Placenta	Placenta
6	chr10:5947200-5981000	Strong transcription	Fetal Intestine Large	intestine
7	chr10:5947400-5981200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr10:5947600-5981000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:5947600-5981000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr10:5947600-5981000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr10:5947600-5981000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr10:5947600-5981200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr10:5948400-5981000	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr10:5948400-5981000	Strong transcription	Stomach Smooth Muscle	stomach
15	chr10:5948600-5981000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr10:5948800-5981000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr10:5948800-5981000	Strong transcription	Duodenum Mucosa	Duodenum
18	chr10:5948800-5981600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr10:5950000-5980400	Strong transcription	Dnd41	blood
20	chr10:5950200-5981000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:5950600-5981000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr10:5950600-5981000	Strong transcription	Lung	lung
23	chr10:5950600-5981000	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr10:5950600-5981200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr10:5950800-5980600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr10:5950800-5980800	Strong transcription	GM12878-XiMat	blood
27	chr10:5952000-5985000	Weak transcription	Stomach Mucosa	stomach
28	chr10:5955000-5981400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:5960600-5977800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr10:5960600-5977800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr10:5960600-5981200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr10:5961000-5981200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr10:5965800-5981000	Strong transcription	A549	lung
34	chr10:5966200-5983600	Weak transcription	Right Atrium	heart
35	chr10:5969400-5982800	Strong transcription	Fetal Stomach	stomach
36	chr10:5969600-5977800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr10:5969600-5987800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr10:5969600-6012000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr10:5969800-5980800	Strong transcription	HSMMtube	muscle
40	chr10:5969800-5981000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr10:5969800-5981200	Strong transcription	Fetal Muscle Leg	muscle
42	chr10:5970000-5981600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr10:5970400-5981000	Strong transcription	Osteobl	bone
44	chr10:5971200-5981000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr10:5971400-5978400	Weak transcription	Fetal Brain Male	brain
46	chr10:5971400-6013200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr10:5971800-5983400	Weak transcription	Psoas Muscle	Psoas
48	chr10:5972000-5977400	Weak transcription	Brain Angular Gyrus	brain
49	chr10:5972200-5981000	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr10:5972400-5978200	Weak transcription	Fetal Kidney	kidney

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