Variant report

Variant	rs5749298
Chromosome Location	chr22:31941032-31941033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	22:31936958-31958600..22:32053085-32061138	Hela-S3	cervix:
2	22:31936958-31958600..22:32162110-32166713	GM12878	blood:
3	22:31936958-31958600..22:32292186-32294405	K562	blood:
4	22:31936958-31958600..22:32188129-32210582	K562	blood:
5	22:31936958-31958600..22:33262063-33266567	K562	blood:
6	22:31936958-31958600..22:32477762-32487457	Hela-S3	cervix:
7	22:31936958-31958600..22:32342898-32343477	GM12878	blood:
8	22:31936958-31958600..22:31978142-31983723	K562	blood:
9	22:31936958-31958600..22:32764253-32784733	K562	blood:
10	22:31936958-31958600..22:32740683-32750950	Hela-S3	cervix:
11	22:31936958-31958600..22:32170492-32188129	GM12878	blood:
12	22:31936958-31958600..22:32750950-32761732	Hela-S3	cervix:
13	22:31936958-31958600..22:32228866-32235273	K562	blood:
14	22:31864703-31891033..22:31936958-31958600	GM12878	blood:
15	22:31836635-31847259..22:31936958-31958600	GM12878	blood:
16	22:31936958-31958600..22:32868055-32872511	K562	blood:
17	22:31936958-31958600..22:32012966-32043914	GM12878	blood:
18	22:31936958-31958600..22:32264718-32278135	Hela-S3	cervix:
19	22:31936958-31958600..22:32594665-32606395	K562	blood:
20	22:31936958-31958600..22:32860159-32865649	K562	blood:
21	22:31936958-31958600..22:32338420-32342898	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198089	Chromatin interaction
ENSG00000184459	Chromatin interaction
ENSG00000128253	Chromatin interaction
ENSG00000241954	Chromatin interaction
ENSG00000185666	Chromatin interaction
ENSG00000254127	Chromatin interaction
ENSG00000252909	Chromatin interaction
ENSG00000100170	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000100225	Chromatin interaction
ENSG00000100150	Chromatin interaction
ENSG00000232218	Chromatin interaction
ENSG00000128254	Chromatin interaction
ENSG00000199248	Chromatin interaction
ENSG00000230736	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000205853	Chromatin interaction
ENSG00000243519	Chromatin interaction
ENSG00000271093	Chromatin interaction
ENSG00000128276	Chromatin interaction
ENSG00000242082	Chromatin interaction
ENSG00000128245	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1018490	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs1543416	0.82[JPT][hapmap]
rs1968023	0.83[CEU][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap]
rs2273249	0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2273251	0.80[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2899164	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs34538851	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4603880	0.83[GIH][hapmap];1.00[LWK][hapmap];0.84[TSI][hapmap]
rs4820983	0.82[JPT][hapmap]
rs5749283	0.85[ASN][1000 genomes]
rs5749286	0.82[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749291	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5749295	0.86[ASN][1000 genomes]
rs5753601	0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs5753618	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap]
rs5753621	0.84[JPT][hapmap]
rs5753632	0.80[CEU][hapmap]
rs5753639	0.80[CEU][hapmap]
rs5753648	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5753659	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5753661	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753664	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753665	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753666	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753669	0.82[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753671	0.82[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5753686	0.82[JPT][hapmap]
rs5753698	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs5753723	0.83[CEU][hapmap];1.00[LWK][hapmap];0.81[TSI][hapmap]
rs5998058	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs5998067	0.82[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs714909	0.85[GIH][hapmap];1.00[LWK][hapmap];0.84[TSI][hapmap]
rs7284622	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7285619	1.00[ASW][hapmap];0.80[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs738657	0.80[CEU][hapmap]
rs8138525	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs8142121	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8142355	1.00[LWK][hapmap]
rs9606839	1.00[ASW][hapmap];0.80[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs9606843	1.00[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs9606846	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9606847	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9606848	0.82[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9606852	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9609295	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9609296	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9609297	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9609299	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9609301	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9609303	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9609304	0.82[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9609329	1.00[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][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	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
3	nsv914978	chr22:31897795-31942770	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5749298	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs5749298	SFI1	cis	cerebellum	SCAN
rs5749298	PISD	cis	cerebellum	SCAN
rs5749298	SFI1	cis	Thyroid	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31893400-31971200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr22:31893600-31946600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr22:31893600-31970000	Weak transcription	Colonic Mucosa	Colon
4	chr22:31893800-31945600	Weak transcription	Brain Anterior Caudate	brain
5	chr22:31894000-31946600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr22:31894000-31946600	Weak transcription	Fetal Brain Female	brain
7	chr22:31904400-31944200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr22:31905200-31957200	Weak transcription	A549	lung
9	chr22:31905600-31946200	Weak transcription	Esophagus	oesophagus
10	chr22:31907400-31946400	Weak transcription	Brain Germinal Matrix	brain
11	chr22:31907400-31946600	Weak transcription	Left Ventricle	heart
12	chr22:31907600-31946200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr22:31907800-31942800	Weak transcription	Fetal Intestine Large	intestine
14	chr22:31911800-31946000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr22:31921800-31942800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr22:31923000-31945800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr22:31924000-31943600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr22:31925000-31946200	Weak transcription	Adipose Nuclei	Adipose
19	chr22:31925200-31942000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr22:31925600-31942800	Weak transcription	Lung	lung
21	chr22:31925800-31957200	Weak transcription	Brain Angular Gyrus	brain
22	chr22:31926800-31946200	Weak transcription	Fetal Muscle Leg	muscle
23	chr22:31926800-31950200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr22:31927000-31946200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr22:31927000-31946200	Weak transcription	Liver	Liver
26	chr22:31927000-31946400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr22:31927200-31946000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr22:31927200-31946400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr22:31927400-31945600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr22:31927400-31946200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr22:31927400-31946800	Weak transcription	HSMM	muscle
32	chr22:31927400-31961400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr22:31927400-31970000	Weak transcription	NH-A	brain
34	chr22:31927400-31970200	Weak transcription	Fetal Lung	lung
35	chr22:31927400-31979400	Weak transcription	NHDF-Ad	bronchial
36	chr22:31927400-31980000	Weak transcription	HSMMtube	muscle
37	chr22:31927600-31974200	Weak transcription	Small Intestine	intestine
38	chr22:31928200-31948800	Weak transcription	Osteobl	bone
39	chr22:31928600-31942200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr22:31928800-31944400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr22:31929000-31942800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr22:31929000-31945600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr22:31929000-31946600	Weak transcription	NHLF	lung
44	chr22:31929000-31953600	Weak transcription	Colon Smooth Muscle	Colon
45	chr22:31929200-31945400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr22:31929200-31946000	Weak transcription	Aorta	Aorta
47	chr22:31929800-31985600	Weak transcription	Fetal Kidney	kidney
48	chr22:31933200-31971000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr22:31933600-31943000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr22:31933600-31946800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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