Variant report

Variant	rs5998471
Chromosome Location	chr22:32786217-32786218
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	22:32162110-32166713..22:32784733-32787968	Hela-S3	cervix:
2	22:32292186-32294405..22:32784733-32787968	K562	blood:
3	22:32477762-32487457..22:32784733-32787968	Hela-S3	cervix:
4	22:32170492-32188129..22:32784733-32787968	K562	blood:
5	22:32784733-32787968..22:33452523-33459358	Hela-S3	cervix:
6	22:31836635-31847259..22:32784733-32787968	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000100150	Chromatin interaction
ENSG00000100170	Chromatin interaction
ENSG00000185666	Chromatin interaction
ENSG00000184708	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11089564	0.82[CHB][hapmap]
rs11635	0.83[ASN][1000 genomes]
rs16990428	0.86[CHB][hapmap]
rs16990430	0.86[CHB][hapmap]
rs2014356	0.82[CHB][hapmap]
rs2049946	0.87[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs2049947	0.85[ASN][1000 genomes]
rs2072815	0.91[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2072816	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs2076041	0.83[ASN][1000 genomes]
rs2076044	0.87[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2076045	0.86[CHB][hapmap]
rs2076048	0.83[JPT][hapmap]
rs2076049	0.83[JPT][hapmap]
rs2142720	0.80[CHB][hapmap]
rs2281034	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2281035	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs2281036	0.91[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.95[ASN][1000 genomes]
rs2294311	0.82[ASN][1000 genomes]
rs2294312	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294313	0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2294314	0.82[ASN][1000 genomes]
rs2413113	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4140572	0.95[CHB][hapmap]
rs5749414	0.87[CHB][hapmap]
rs5749416	0.91[CHB][hapmap]
rs5749421	0.96[ASN][1000 genomes]
rs5749426	0.95[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.97[ASN][1000 genomes]
rs5749427	0.84[ASN][1000 genomes]
rs5749428	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs5749429	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs5749432	0.83[JPT][hapmap]
rs5749436	0.82[CHB][hapmap]
rs5754020	0.86[JPT][hapmap]
rs5754060	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5754063	0.95[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.96[ASN][1000 genomes]
rs5754065	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs5754066	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs59895149	0.83[ASN][1000 genomes]
rs5994562	0.87[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs5998440	0.82[JPT][hapmap]
rs5998475	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs5998478	0.87[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs60953467	0.81[ASN][1000 genomes]
rs713790	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs7287452	0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs737779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742096	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs9609518	0.82[TSI][hapmap]

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	esv2422247	chr22:32486448-32788258	Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1064737	chr22:32603912-32829725	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv1066118	chr22:32779078-32815334	Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5998471	RAB27A	trans	cerebellum	SCAN
rs5998471	CCDC157	cis	parietal	SCAN
rs5998471	OSBP2	cis	cerebellum	SCAN
rs5998471	RFPL3S	Cis_1M	lymphoblastoid	RTeQTL
rs5998471	C22orf28	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32762800-32788200	Weak transcription	Psoas Muscle	Psoas
2	chr22:32777200-32793800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr22:32780000-32790400	Weak transcription	Fetal Brain Male	brain
4	chr22:32780800-32789000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr22:32780800-32806400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr22:32780800-32806400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr22:32781200-32787000	Strong transcription	Primary T cells from cord blood	blood
8	chr22:32781200-32793600	Strong transcription	Fetal Kidney	kidney
9	chr22:32781200-32798200	Strong transcription	Thymus	Thymus
10	chr22:32781200-32799200	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr22:32781200-32801200	Strong transcription	Fetal Stomach	stomach
12	chr22:32781200-32802200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr22:32781200-32803200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr22:32781200-32804000	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr22:32781200-32804200	Strong transcription	Stomach Smooth Muscle	stomach
16	chr22:32781200-32804600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr22:32781200-32804600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr22:32781200-32804800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr22:32781200-32805000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr22:32781200-32805400	Strong transcription	Fetal Muscle Leg	muscle
21	chr22:32781200-32806600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr22:32781400-32786600	Strong transcription	Brain Germinal Matrix	brain
23	chr22:32781400-32786600	Strong transcription	A549	lung
24	chr22:32781400-32787400	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr22:32781400-32787400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr22:32781400-32787400	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr22:32781400-32793000	Strong transcription	Fetal Intestine Small	intestine
28	chr22:32781400-32798200	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr22:32781400-32798200	Strong transcription	Brain Anterior Caudate	brain
30	chr22:32781400-32798200	Strong transcription	NH-A	brain
31	chr22:32781400-32799200	Strong transcription	Lung	lung
32	chr22:32781400-32801200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr22:32781400-32802600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr22:32781400-32802600	Strong transcription	GM12878-XiMat	blood
35	chr22:32781400-32802600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr22:32781400-32803200	Strong transcription	Adipose Nuclei	Adipose
37	chr22:32781400-32803200	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr22:32781400-32803600	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr22:32781400-32803800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr22:32781400-32803800	Strong transcription	Liver	Liver
41	chr22:32781400-32804400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr22:32781400-32804600	Strong transcription	Fetal Thymus	thymus
43	chr22:32781400-32804600	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr22:32781400-32804600	Strong transcription	Dnd41	blood
45	chr22:32781400-32804800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr22:32781400-32804800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr22:32781400-32804800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr22:32781400-32804800	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr22:32781400-32805000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr22:32781400-32805000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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