Variant report

Variant	rs5998042
Chromosome Location	chr22:31953962-31953963
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:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 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	chr22:31951704..31954634-chr22:31955537..31958557,4	MCF-7	breast:
6	22:31936958-31958600..22:33262063-33266567	K562	blood:
7	22:31936958-31958600..22:32477762-32487457	Hela-S3	cervix:
8	22:31936958-31958600..22:32342898-32343477	GM12878	blood:
9	22:31936958-31958600..22:31978142-31983723	K562	blood:
10	22:31936958-31958600..22:32764253-32784733	K562	blood:
11	22:31936958-31958600..22:32740683-32750950	Hela-S3	cervix:
12	22:31936958-31958600..22:32170492-32188129	GM12878	blood:
13	22:31936958-31958600..22:32750950-32761732	Hela-S3	cervix:
14	22:31936958-31958600..22:32228866-32235273	K562	blood:
15	22:31864703-31891033..22:31936958-31958600	GM12878	blood:
16	22:31836635-31847259..22:31936958-31958600	GM12878	blood:
17	22:31936958-31958600..22:32868055-32872511	K562	blood:
18	22:31936958-31958600..22:32012966-32043914	GM12878	blood:
19	chr22:31952629..31954536-chr22:32025610..32028479,3	MCF-7	breast:
20	22:31936958-31958600..22:32264718-32278135	Hela-S3	cervix:
21	22:31936958-31958600..22:32594665-32606395	K562	blood:
22	22:31936958-31958600..22:32860159-32865649	K562	blood:
23	22:31936958-31958600..22:32338420-32342898	K562	blood:

No data

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

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12170867	0.86[JPT][hapmap]
rs12171042	0.89[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes]
rs12484606	0.84[EUR][1000 genomes]
rs13056823	0.82[EUR][1000 genomes]
rs131233	0.80[YRI][hapmap]
rs14034	0.84[EUR][1000 genomes]
rs1543416	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1916	0.83[MKK][hapmap]
rs2006771	0.86[LWK][hapmap];0.90[YRI][hapmap]
rs2024747	0.82[JPT][hapmap]
rs2092905	0.86[JPT][hapmap]
rs2295242	0.86[JPT][hapmap]
rs2295251	0.95[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs2387	0.86[JPT][hapmap]
rs3818134	0.84[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs4535154	0.80[EUR][1000 genomes]
rs4820976	0.85[EUR][1000 genomes]
rs4820978	0.85[EUR][1000 genomes]
rs4820979	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs4820980	0.84[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs4820981	0.81[EUR][1000 genomes]
rs4820982	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4820983	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5749293	0.82[JPT][hapmap]
rs5749303	0.86[JPT][hapmap]
rs5749304	0.84[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[MKK][hapmap];0.93[EUR][1000 genomes]
rs5749306	0.86[JPT][hapmap]
rs5753667	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs5753680	0.83[EUR][1000 genomes]
rs5753681	0.82[JPT][hapmap]
rs5753686	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5753698	0.82[JPT][hapmap]
rs5753733	0.83[EUR][1000 genomes]
rs5753734	0.89[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs5998002	0.82[MKK][hapmap]
rs5998011	0.83[EUR][1000 genomes]
rs5998032	0.84[EUR][1000 genomes]
rs5998035	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5998054	0.82[TSI][hapmap]
rs5998067	0.87[CHB][hapmap]
rs7287937	0.84[LWK][hapmap];0.86[YRI][hapmap]
rs7289075	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs7291918	0.89[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs738656	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs738702	0.86[JPT][hapmap]
rs761746	0.84[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.82[LWK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap]
rs761747	0.83[EUR][1000 genomes]
rs8461	0.83[GIH][hapmap]
rs9609329	0.82[JPT][hapmap]
rs9621279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9956	0.94[ASW][hapmap];0.95[CEU][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]

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	nsv964622	chr22:31953885-31956099	Strong transcription Weak transcription Enhancers	TF binding region Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5998042	SFI1	cis	cerebellum	SCAN

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	chr22:31893600-31970000	Weak transcription	Colonic Mucosa	Colon
3	chr22:31905200-31957200	Weak transcription	A549	lung
4	chr22:31925800-31957200	Weak transcription	Brain Angular Gyrus	brain
5	chr22:31927400-31961400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr22:31927400-31970000	Weak transcription	NH-A	brain
7	chr22:31927400-31970200	Weak transcription	Fetal Lung	lung
8	chr22:31927400-31979400	Weak transcription	NHDF-Ad	bronchial
9	chr22:31927400-31980000	Weak transcription	HSMMtube	muscle
10	chr22:31927600-31974200	Weak transcription	Small Intestine	intestine
11	chr22:31929800-31985600	Weak transcription	Fetal Kidney	kidney
12	chr22:31933200-31971000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr22:31933600-31979600	Weak transcription	HUVEC	blood vessel
14	chr22:31934000-31981000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr22:31935200-31985400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:31935400-31957200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr22:31935600-31970000	Weak transcription	HMEC	breast
18	chr22:31935800-32013200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr22:31941200-31957200	Weak transcription	Right Ventricle	heart
20	chr22:31941400-31981400	Weak transcription	NHEK	skin
21	chr22:31946400-31957200	Weak transcription	Stomach Mucosa	stomach
22	chr22:31946800-31957000	Weak transcription	HepG2	liver
23	chr22:31946800-31957400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr22:31947000-31954600	Weak transcription	Fetal Intestine Small	intestine
25	chr22:31947000-31970200	Weak transcription	Brain Substantia Nigra	brain
26	chr22:31947000-31970200	Weak transcription	Fetal Muscle Leg	muscle
27	chr22:31947200-31955400	Weak transcription	HSMM	muscle
28	chr22:31947200-31969600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr22:31947400-31954400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr22:31947400-31955200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr22:31947400-31957200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr22:31947400-31957200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr22:31947400-31968200	Weak transcription	Brain Germinal Matrix	brain
34	chr22:31947400-31968800	Weak transcription	Gastric	stomach
35	chr22:31947400-31968800	Weak transcription	Pancreas	Pancrea
36	chr22:31947400-31969000	Weak transcription	Fetal Brain Female	brain
37	chr22:31947400-31969000	Weak transcription	Lung	lung
38	chr22:31947400-31969200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr22:31947400-31970200	Weak transcription	Ovary	ovary
40	chr22:31947400-31971000	Weak transcription	Aorta	Aorta
41	chr22:31947400-31972800	Weak transcription	Esophagus	oesophagus
42	chr22:31947600-31957200	Weak transcription	Brain Hippocampus Middle	brain
43	chr22:31947800-31957200	Weak transcription	Brain Anterior Caudate	brain
44	chr22:31947800-31957200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr22:31947800-31961800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr22:31947800-31968800	Weak transcription	Spleen	Spleen
47	chr22:31947800-31969000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr22:31947800-31969200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr22:31947800-31970200	Weak transcription	Fetal Intestine Large	intestine
50	chr22:31947800-31970200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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