Variant report

Variant	rs134657
Chromosome Location	chr22:29490497-29490498
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29490478..29492943-chr22:29507351..29509908,2	K562	blood:
2	chr22:29219559..29221242-chr22:29488785..29491487,2	MCF-7	breast:
3	chr22:29490386..29492445-chr22:29548625..29550170,2	K562	blood:
4	chr22:29468314..29470474-chr22:29489688..29492570,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226772	Chromatin interaction
ENSG00000183762	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12329960	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs134560	0.85[MEX][hapmap]
rs134564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs134577	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs134588	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs134592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs134596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs134598	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs134605	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs134607	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs134608	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs134609	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs134622	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs134630	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs134631	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134637	0.86[GIH][hapmap];0.81[TSI][hapmap]
rs134641	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134644	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134660	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs134664	0.80[AMR][1000 genomes]
rs134666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs134669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs134670	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs134672	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs134676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs134677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs20037	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs4347951	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5752864	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752867	0.83[YRI][hapmap]
rs5752868	0.83[YRI][hapmap]
rs713861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7292708	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs783	0.81[TSI][hapmap]
rs9613819	0.81[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs134657	TBC1D10A	cis	cerebellum	SCAN
rs134657	MORC2	cis	cerebellum	SCAN
rs134657	KREMEN1	cis	Heart Left Ventricle	GTEx
rs134657	EMID1	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29475600-29491000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr22:29475600-29505600	Weak transcription	Spleen	Spleen
3	chr22:29476600-29491000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr22:29476800-29494800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr22:29478800-29498200	Weak transcription	Brain Germinal Matrix	brain
6	chr22:29480600-29498000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr22:29480800-29492400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr22:29483400-29550200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr22:29485800-29492200	Weak transcription	K562	blood
10	chr22:29486000-29491000	Weak transcription	Colonic Mucosa	Colon
11	chr22:29486000-29492600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr22:29486200-29490800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr22:29486200-29491000	Weak transcription	Fetal Brain Female	brain
14	chr22:29486600-29494800	Weak transcription	NHEK	skin
15	chr22:29486600-29519000	Weak transcription	Fetal Brain Male	brain
16	chr22:29487600-29491000	Enhancers	Fetal Lung	lung
17	chr22:29487600-29491000	Enhancers	Ovary	ovary
18	chr22:29488400-29492400	Weak transcription	Right Ventricle	heart
19	chr22:29488400-29521200	Weak transcription	Lung	lung
20	chr22:29488600-29494800	Weak transcription	Placenta	Placenta
21	chr22:29488800-29491000	Weak transcription	Gastric	stomach
22	chr22:29488800-29491000	Weak transcription	Right Atrium	heart
23	chr22:29488800-29492400	Weak transcription	Pancreas	Pancrea
24	chr22:29489000-29490800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr22:29489000-29492600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr22:29489000-29494800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr22:29489200-29494800	Weak transcription	Adipose Nuclei	Adipose
28	chr22:29489400-29491000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr22:29489400-29491000	Weak transcription	Stomach Mucosa	stomach
30	chr22:29489600-29492000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr22:29489600-29492200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr22:29489600-29492600	Strong transcription	Esophagus	oesophagus
33	chr22:29489600-29492800	Weak transcription	Small Intestine	intestine
34	chr22:29489600-29493000	Enhancers	HepG2	liver
35	chr22:29489600-29499800	Strong transcription	Dnd41	blood
36	chr22:29489800-29491000	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr22:29489800-29491000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr22:29489800-29492400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr22:29489800-29492600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr22:29489800-29493000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr22:29490000-29491000	Weak transcription	Fetal Intestine Large	intestine
42	chr22:29490000-29491000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr22:29490000-29492000	Strong transcription	Fetal Thymus	thymus
44	chr22:29490000-29492400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr22:29490000-29492600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr22:29490000-29492800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr22:29490000-29501600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr22:29490000-29505200	Weak transcription	Aorta	Aorta
49	chr22:29490000-29514000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr22:29490200-29490600	Genic enhancers	Fetal Stomach	stomach

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