Variant report

Variant	rs5749416
Chromosome Location	chr22:32777123-32777124
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr22:32777089-32777240	T-47D	breast:	n/a	chr22:32777167-32777182
2	JUND	chr22:32777034-32777376	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	22:31829733-31836635..22:32764253-32784733	K562	blood:
2	22:31936958-31958600..22:32764253-32784733	K562	blood:
3	chr22:32774801..32777723-chr22:32782145..32784494,2	MCF-7	breast:
4	22:32529813-32538538..22:32764253-32784733	H1-hESC	embryonic stem cell:	embryo
5	chr22:32774995..32777727-chr22:32778059..32780471,2	K562	blood:
6	22:32513817-32522138..22:32764253-32784733	H1-hESC	embryonic stem cell:	embryo
7	22:32360288-32405313..22:32764253-32784733	K562	blood:

No data

Variant related genes	Relation type
ENSG00000241954	TF binding region
ENSG00000241954	Chromatin interaction
ENSG00000232218	Chromatin interaction
ENSG00000239674	Chromatin interaction
ENSG00000232707	Chromatin interaction
ENSG00000214093	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000240647	Chromatin interaction
ENSG00000230866	Chromatin interaction
ENSG00000234479	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs11089557	0.82[ASN][1000 genomes]
rs11089564	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11635	0.92[ASN][1000 genomes]
rs11912349	0.81[ASN][1000 genomes]
rs12160141	0.84[ASN][1000 genomes]
rs12160986	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs12530	0.84[ASW][hapmap]
rs12628702	0.83[ASN][1000 genomes]
rs136471	0.82[ASN][1000 genomes]
rs1543320	0.81[CHD][hapmap]
rs16987625	0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs16990258	0.84[ASN][1000 genomes]
rs16990262	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs16990269	0.84[ASN][1000 genomes]
rs16990428	0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16990430	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2014356	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2072815	0.91[CHB][hapmap]
rs2072816	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]
rs2076041	0.92[ASN][1000 genomes]
rs2076045	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2142720	0.81[CHB][hapmap]
rs2281034	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.99[ASN][1000 genomes]
rs2281035	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[ASN][1000 genomes]
rs2281036	0.83[CHB][hapmap]
rs2294311	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2294313	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2294314	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2413110	0.81[ASN][1000 genomes]
rs2413113	0.91[CHB][hapmap]
rs2899185	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4140572	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs45593940	0.83[ASN][1000 genomes]
rs5749409	0.82[CHB][hapmap];0.85[CHD][hapmap];0.84[ASN][1000 genomes]
rs5749410	0.84[ASN][1000 genomes]
rs5749411	0.84[ASN][1000 genomes]
rs5749412	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs5749413	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs5749414	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs5749426	0.87[CHB][hapmap]
rs5749427	0.91[ASN][1000 genomes]
rs5749428	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5749429	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs5749433	0.83[ASN][1000 genomes]
rs5749436	0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs5754001	0.81[ASN][1000 genomes]
rs5754003	0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs5754005	0.81[ASN][1000 genomes]
rs5754006	0.82[ASN][1000 genomes]
rs5754007	0.82[ASN][1000 genomes]
rs5754008	0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs5754009	0.83[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs5754010	0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs5754011	0.82[ASN][1000 genomes]
rs5754012	0.82[ASN][1000 genomes]
rs5754017	0.84[ASN][1000 genomes]
rs5754018	0.83[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs5754019	0.83[ASN][1000 genomes]
rs5754021	0.81[ASN][1000 genomes]
rs5754023	0.84[ASN][1000 genomes]
rs5754025	0.84[ASN][1000 genomes]
rs5754027	0.81[JPT][hapmap]
rs5754029	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs5754030	0.81[JPT][hapmap]
rs5754032	0.84[ASN][1000 genomes]
rs5754033	0.84[ASN][1000 genomes]
rs5754035	0.83[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs5754036	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs5754037	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs5754039	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs5754040	0.81[JPT][hapmap]
rs5754042	0.83[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs5754044	0.81[JPT][hapmap]
rs5754045	0.83[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs5754047	0.84[ASN][1000 genomes]
rs5754048	0.82[ASN][1000 genomes]
rs5754050	0.81[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs5754063	0.87[CHB][hapmap]
rs5754065	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs5754066	0.87[CHB][hapmap]
rs58028985	0.83[ASN][1000 genomes]
rs59895149	0.92[ASN][1000 genomes]
rs5998434	0.81[ASN][1000 genomes]
rs5998451	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs5998453	0.84[ASN][1000 genomes]
rs5998456	0.80[JPT][hapmap]
rs5998457	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs5998459	0.81[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs5998463	0.81[JPT][hapmap]
rs5998471	0.91[CHB][hapmap]
rs5998475	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs713790	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs72137940	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72617300	0.81[ASN][1000 genomes]
rs72617301	0.81[ASN][1000 genomes]
rs72617302	0.81[ASN][1000 genomes]
rs72620403	0.81[ASN][1000 genomes]
rs72620404	0.81[ASN][1000 genomes]
rs72620407	0.81[ASN][1000 genomes]
rs72620408	0.81[ASN][1000 genomes]
rs7287452	0.87[CHB][hapmap]
rs7291359	0.84[ASN][1000 genomes]
rs734809	0.80[CEU][hapmap]
rs737779	0.91[CHB][hapmap]
rs738267	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs742096	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[ASN][1000 genomes]
rs9609527	0.84[ASW][hapmap];0.80[CEU][hapmap]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5749416	C22orf28	cis	cerebellum	SCAN
rs5749416	RFPL3S	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32755800-32781600	Weak transcription	Ovary	ovary
2	chr22:32762800-32788200	Weak transcription	Psoas Muscle	Psoas
3	chr22:32772000-32781200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr22:32772200-32781400	Weak transcription	Fetal Intestine Small	intestine
5	chr22:32772600-32781400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr22:32772800-32780800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr22:32772800-32781400	Weak transcription	Brain Germinal Matrix	brain
8	chr22:32772800-32781600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr22:32773200-32781400	Weak transcription	Gastric	stomach
10	chr22:32773200-32781400	Weak transcription	Lung	lung
11	chr22:32773800-32781600	Weak transcription	Esophagus	oesophagus
12	chr22:32774000-32782000	Weak transcription	Primary B cells from cord blood	blood
13	chr22:32774400-32781200	Weak transcription	Primary T cells from cord blood	blood
14	chr22:32774400-32781400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr22:32774600-32780800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:32775000-32783400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr22:32775200-32781200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr22:32775200-32781200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr22:32775200-32781400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr22:32775200-32781400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr22:32775200-32781400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr22:32775200-32782000	Weak transcription	HMEC	breast
23	chr22:32775200-32782200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr22:32775200-32782200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr22:32775200-32782200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr22:32775200-32782400	Weak transcription	Brain Hippocampus Middle	brain
27	chr22:32775200-32782600	Weak transcription	Right Ventricle	heart
28	chr22:32775200-32783200	Weak transcription	HepG2	liver
29	chr22:32775400-32781200	Weak transcription	Fetal Muscle Leg	muscle
30	chr22:32775400-32781400	Weak transcription	Brain Anterior Caudate	brain
31	chr22:32775400-32781400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr22:32775400-32781400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr22:32775400-32781600	Weak transcription	Brain Angular Gyrus	brain
34	chr22:32775400-32781600	Weak transcription	Brain Substantia Nigra	brain
35	chr22:32775400-32781600	Weak transcription	Spleen	Spleen
36	chr22:32775400-32783000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr22:32775400-32783400	Weak transcription	K562	blood
38	chr22:32775600-32781200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr22:32775600-32781400	Weak transcription	Adipose Nuclei	Adipose
40	chr22:32775600-32781400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr22:32775600-32781400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr22:32775600-32783400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr22:32776600-32781400	Weak transcription	Fetal Intestine Large	intestine
44	chr22:32777000-32777200	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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