Variant report

Variant	rs5749135
Chromosome Location	chr22:31011906-31011907
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31001608..31004689-chr22:31008894..31012791,3	K562	blood:

Variant related genes	Relation type
ENSG00000100029	Chromatin interaction
ENSG00000185339	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11703570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs13054912	0.80[ASN][1000 genomes]
rs13055009	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13056378	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13057127	0.83[ASN][1000 genomes]
rs1544468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2301955	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2301957	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2301958	0.93[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.83[ASN][1000 genomes]
rs4353747	0.83[ASN][1000 genomes]
rs4820882	0.94[ASN][1000 genomes]
rs4820888	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4820890	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56132790	0.83[ASN][1000 genomes]
rs5749131	0.81[CHB][hapmap]
rs5749132	0.99[ASN][1000 genomes]
rs5749134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749137	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749142	0.83[ASN][1000 genomes]
rs5749143	0.83[ASN][1000 genomes]
rs5749145	0.83[ASN][1000 genomes]
rs5749148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5753229	0.92[ASN][1000 genomes]
rs5753234	1.00[ASN][1000 genomes]
rs5753246	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5753247	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs5753260	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5997703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997709	0.82[ASN][1000 genomes]
rs5997710	0.82[ASN][1000 genomes]
rs5997727	0.93[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap]
rs7286680	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7289553	0.83[ASN][1000 genomes]
rs731990	0.83[ASN][1000 genomes]
rs731991	0.83[ASN][1000 genomes]
rs740233	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs740235	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8630	0.93[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap]
rs9609017	0.94[ASN][1000 genomes]
rs9621047	0.81[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[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	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv834175	chr22:30976624-31089545	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5749135	ZNRF3	cis	cerebellum	SCAN
rs5749135	PES1	cis	parietal	SCAN
rs5749135	CRYBB3	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31003200-31031200	Weak transcription	Aorta	Aorta
2	chr22:31003800-31030600	Weak transcription	Thymus	Thymus
3	chr22:31004200-31013400	Weak transcription	Pancreas	Pancrea
4	chr22:31004400-31020200	Weak transcription	Fetal Kidney	kidney
5	chr22:31005000-31022200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr22:31005600-31012200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr22:31006000-31019200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr22:31006000-31020800	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr22:31006000-31023200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr22:31006000-31023200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr22:31006000-31030400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr22:31006000-31030600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr22:31006000-31030600	Weak transcription	Colonic Mucosa	Colon
14	chr22:31006200-31017400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr22:31006200-31017400	Strong transcription	Fetal Stomach	stomach
16	chr22:31006200-31019400	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr22:31006200-31023800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr22:31006200-31030600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr22:31006400-31013600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr22:31006400-31015000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr22:31006400-31017000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr22:31006400-31023000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr22:31006400-31023200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr22:31006400-31023400	Strong transcription	Fetal Intestine Small	intestine
25	chr22:31006600-31017000	Strong transcription	Brain Germinal Matrix	brain
26	chr22:31006600-31020000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr22:31006600-31030400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr22:31006800-31030200	Weak transcription	Placenta	Placenta
29	chr22:31007000-31012200	Strong transcription	Fetal Intestine Large	intestine
30	chr22:31007000-31017200	Strong transcription	Liver	Liver
31	chr22:31007000-31030600	Weak transcription	Fetal Brain Male	brain
32	chr22:31007200-31019200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr22:31007600-31030200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr22:31008000-31030400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr22:31008400-31023200	Strong transcription	Adipose Nuclei	Adipose
36	chr22:31008600-31012000	Strong transcription	Fetal Brain Female	brain
37	chr22:31008600-31012200	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr22:31008600-31014000	Strong transcription	Brain Substantia Nigra	brain
39	chr22:31008800-31012000	Strong transcription	Brain Cingulate Gyrus	brain
40	chr22:31008800-31012000	Strong transcription	Brain Hippocampus Middle	brain
41	chr22:31008800-31013800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr22:31008800-31019000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr22:31009000-31012200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr22:31009600-31012000	Strong transcription	Brain Angular Gyrus	brain
45	chr22:31009600-31017000	Strong transcription	Stomach Smooth Muscle	stomach
46	chr22:31009800-31012000	Strong transcription	Brain Anterior Caudate	brain
47	chr22:31009800-31012200	Strong transcription	Gastric	stomach
48	chr22:31009800-31015800	Strong transcription	Fetal Lung	lung
49	chr22:31010000-31012200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr22:31010000-31012200	Strong transcription	Colon Smooth Muscle	Colon

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