Variant report

Variant	rs2072816
Chromosome Location	chr22:32790398-32790399
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:32787177..32791195-chr22:32793351..32796460,3	K562	blood:
2	chr22:32789382..32790946-chr22:32793336..32795343,2	MCF-7	breast:
3	22:32096851-32100847..22:32787968-32792766	K562	blood:
4	22:32477762-32487457..22:32787968-32792766	Hela-S3	cervix:
5	22:31864703-31891033..22:32787968-32792766	K562	blood:
6	chr22:32788346..32791195-chr22:32793351..32795466,2	K562	blood:
7	22:32264718-32278135..22:32787968-32792766	GM12878	blood:
8	22:32170492-32188129..22:32787968-32792766	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000198089	Chromatin interaction
ENSG00000183530	Chromatin interaction
ENSG00000100170	Chromatin interaction
ENSG00000100220	Chromatin interaction
ENSG00000100150	Chromatin interaction
ENSG00000199248	Chromatin interaction
ENSG00000184708	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11089564	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs11635	0.97[ASN][1000 genomes]
rs11912349	0.88[ASN][1000 genomes]
rs11914186	0.85[YRI][hapmap]
rs12160986	0.86[JPT][hapmap]
rs12628702	0.90[ASN][1000 genomes]
rs16987625	0.86[JPT][hapmap]
rs16990262	0.86[JPT][hapmap]
rs16990370	0.84[YRI][hapmap]
rs16990428	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16990430	0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2014356	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2076041	0.99[ASN][1000 genomes]
rs2076045	0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2281034	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2281035	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2294311	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294312	0.83[ASN][1000 genomes]
rs2294313	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294314	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2899185	0.86[JPT][hapmap]
rs4140572	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs5749412	0.81[JPT][hapmap]
rs5749413	0.86[JPT][hapmap]
rs5749414	0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs5749416	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749421	0.81[ASN][1000 genomes]
rs5749426	0.83[CHB][hapmap]
rs5749427	0.98[ASN][1000 genomes]
rs5749428	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749429	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs5749433	0.90[ASN][1000 genomes]
rs5749436	0.95[JPT][hapmap]
rs5754003	0.82[JPT][hapmap]
rs5754008	0.86[JPT][hapmap]
rs5754009	0.86[JPT][hapmap]
rs5754010	0.86[JPT][hapmap]
rs5754018	0.86[JPT][hapmap]
rs5754027	0.81[JPT][hapmap]
rs5754029	0.85[JPT][hapmap]
rs5754030	0.82[JPT][hapmap]
rs5754035	0.86[JPT][hapmap]
rs5754036	0.81[JPT][hapmap]
rs5754037	0.81[JPT][hapmap]
rs5754039	0.86[JPT][hapmap]
rs5754040	0.82[JPT][hapmap]
rs5754042	0.86[JPT][hapmap]
rs5754044	0.82[JPT][hapmap]
rs5754045	0.86[JPT][hapmap]
rs5754050	0.85[JPT][hapmap]
rs5754063	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs5754065	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs5754066	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs59895149	0.97[ASN][1000 genomes]
rs5998451	0.81[JPT][hapmap]
rs5998457	0.85[JPT][hapmap]
rs5998459	0.86[JPT][hapmap]
rs5998463	0.82[JPT][hapmap]
rs5998471	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs5998475	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs713790	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs72137940	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7286662	0.84[YRI][hapmap]
rs737779	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs738267	0.81[JPT][hapmap]
rs742096	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2072816	RFPL3S	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32777200-32793800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:32780000-32790400	Weak transcription	Fetal Brain Male	brain
3	chr22:32780800-32806400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr22:32780800-32806400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:32781200-32793600	Strong transcription	Fetal Kidney	kidney
6	chr22:32781200-32798200	Strong transcription	Thymus	Thymus
7	chr22:32781200-32799200	Strong transcription	Duodenum Smooth Muscle	Duodenum
8	chr22:32781200-32801200	Strong transcription	Fetal Stomach	stomach
9	chr22:32781200-32802200	Strong transcription	Primary B cells from peripheral blood	blood
10	chr22:32781200-32803200	Strong transcription	Duodenum Mucosa	Duodenum
11	chr22:32781200-32804000	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr22:32781200-32804200	Strong transcription	Stomach Smooth Muscle	stomach
13	chr22:32781200-32804600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr22:32781200-32804600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr22:32781200-32804800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr22:32781200-32805000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr22:32781200-32805400	Strong transcription	Fetal Muscle Leg	muscle
18	chr22:32781200-32806600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr22:32781400-32793000	Strong transcription	Fetal Intestine Small	intestine
20	chr22:32781400-32798200	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr22:32781400-32798200	Strong transcription	Brain Anterior Caudate	brain
22	chr22:32781400-32798200	Strong transcription	NH-A	brain
23	chr22:32781400-32799200	Strong transcription	Lung	lung
24	chr22:32781400-32801200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr22:32781400-32802600	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr22:32781400-32802600	Strong transcription	GM12878-XiMat	blood
27	chr22:32781400-32802600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr22:32781400-32803200	Strong transcription	Adipose Nuclei	Adipose
29	chr22:32781400-32803200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr22:32781400-32803600	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr22:32781400-32803800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr22:32781400-32803800	Strong transcription	Liver	Liver
33	chr22:32781400-32804400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr22:32781400-32804600	Strong transcription	Fetal Thymus	thymus
35	chr22:32781400-32804600	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr22:32781400-32804600	Strong transcription	Dnd41	blood
37	chr22:32781400-32804800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr22:32781400-32804800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr22:32781400-32804800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr22:32781400-32804800	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr22:32781400-32805000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr22:32781400-32805000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr22:32781400-32805000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr22:32781400-32805000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr22:32781400-32805000	Strong transcription	Fetal Intestine Large	intestine
46	chr22:32781400-32805000	Strong transcription	Fetal Lung	lung
47	chr22:32781400-32805000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr22:32781400-32805000	Strong transcription	Left Ventricle	heart
49	chr22:32781400-32805000	Strong transcription	Osteobl	bone
50	chr22:32781400-32805200	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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