Variant report

Variant	rs2092905
Chromosome Location	chr22:31966274-31966275
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	22:31961151-31976153..22:33253287-33262063	K562	blood:
2	22:31961151-31976153..22:32513817-32522138	K562	blood:
3	22:31961151-31976153..22:33030812-33041554	K562	blood:
4	22:31961151-31976153..22:32284948-32287956	K562	blood:

Variant related genes	Relation type
ENSG00000251890	Chromatin interaction
ENSG00000183531	Chromatin interaction
ENSG00000227813	Chromatin interaction
ENSG00000234479	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1044085	0.81[JPT][hapmap]
rs10775716	0.88[ASN][1000 genomes]
rs11089512	0.86[JPT][hapmap]
rs12170867	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12171042	0.95[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.82[ASN][1000 genomes]
rs12627933	0.86[CHB][hapmap];1.00[MEX][hapmap]
rs140078	0.82[MEX][hapmap]
rs140081	0.82[MEX][hapmap]
rs1543416	0.81[JPT][hapmap]
rs2024747	0.95[JPT][hapmap]
rs2236033	0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs2295242	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2295251	0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.82[ASN][1000 genomes]
rs2387	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3804087	0.83[MEX][hapmap]
rs3818134	0.86[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs4820051	0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs4820979	0.88[ASW][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap]
rs4820980	0.84[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs4820983	0.81[JPT][hapmap]
rs5749293	0.80[CHD][hapmap];0.95[JPT][hapmap]
rs5749303	0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs5749304	0.90[CEU][hapmap];0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs5749306	0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs5753667	0.86[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap]
rs5753681	0.80[CHD][hapmap];0.95[JPT][hapmap]
rs5753684	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5753686	0.81[JPT][hapmap]
rs5753690	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5753691	0.88[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs5753713	0.82[ASN][1000 genomes]
rs5753714	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753715	0.88[ASN][1000 genomes]
rs5753734	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap]
rs5994415	0.90[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5998042	0.86[JPT][hapmap]
rs5998054	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5998086	0.83[MEX][hapmap]
rs7289075	0.95[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7291918	0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.84[ASN][1000 genomes]
rs738656	0.86[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap]
rs738684	0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs738702	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs761746	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap]
rs761747	0.82[ASN][1000 genomes]
rs8461	0.81[JPT][hapmap];0.94[MEX][hapmap]
rs9956	0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.94[MEX][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	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	nsv914979	chr22:31964043-31990184	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv914980	chr22:31966274-32024980	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2092905	PATZ1	cis	Liver	GTEx
rs2092905	AK055495	cis	multi-tissue	Pritchard
rs2092905	NM_032757	cis	multi-tissue	Pritchard

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	chr22:31927400-31970000	Weak transcription	NH-A	brain
4	chr22:31927400-31970200	Weak transcription	Fetal Lung	lung
5	chr22:31927400-31979400	Weak transcription	NHDF-Ad	bronchial
6	chr22:31927400-31980000	Weak transcription	HSMMtube	muscle
7	chr22:31927600-31974200	Weak transcription	Small Intestine	intestine
8	chr22:31929800-31985600	Weak transcription	Fetal Kidney	kidney
9	chr22:31933200-31971000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr22:31933600-31979600	Weak transcription	HUVEC	blood vessel
11	chr22:31934000-31981000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr22:31935200-31985400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:31935600-31970000	Weak transcription	HMEC	breast
14	chr22:31935800-32013200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr22:31941400-31981400	Weak transcription	NHEK	skin
16	chr22:31947000-31970200	Weak transcription	Brain Substantia Nigra	brain
17	chr22:31947000-31970200	Weak transcription	Fetal Muscle Leg	muscle
18	chr22:31947200-31969600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr22:31947400-31968200	Weak transcription	Brain Germinal Matrix	brain
20	chr22:31947400-31968800	Weak transcription	Gastric	stomach
21	chr22:31947400-31968800	Weak transcription	Pancreas	Pancrea
22	chr22:31947400-31969000	Weak transcription	Fetal Brain Female	brain
23	chr22:31947400-31969000	Weak transcription	Lung	lung
24	chr22:31947400-31969200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr22:31947400-31970200	Weak transcription	Ovary	ovary
26	chr22:31947400-31971000	Weak transcription	Aorta	Aorta
27	chr22:31947400-31972800	Weak transcription	Esophagus	oesophagus
28	chr22:31947800-31968800	Weak transcription	Spleen	Spleen
29	chr22:31947800-31969000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr22:31947800-31969200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr22:31947800-31970200	Weak transcription	Fetal Intestine Large	intestine
32	chr22:31947800-31970200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr22:31947800-31971000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr22:31947800-31971200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr22:31947800-32009600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr22:31948000-31968400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr22:31948000-31973400	Weak transcription	Liver	Liver
38	chr22:31948200-31968800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr22:31948200-31980000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr22:31949200-31971800	Weak transcription	NHLF	lung
41	chr22:31949200-31973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr22:31949200-31981600	Weak transcription	Left Ventricle	heart
43	chr22:31949400-32014400	Weak transcription	Hela-S3	cervix
44	chr22:31949600-31977800	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr22:31949800-31976400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr22:31952800-31967400	Strong transcription	Fetal Thymus	thymus
47	chr22:31954000-31968800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr22:31954000-31968800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr22:31954000-31968800	Weak transcription	Colon Smooth Muscle	Colon
50	chr22:31954000-31970000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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