Variant report

Variant	rs10422762
Chromosome Location	chr19:36157167-36157168
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:36157131-36157209	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr19:36156492-36158098	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:36157027-36157675	ECC-1	luminal epithelium:	n/a	n/a
4	ELF1	chr19:36157018-36157477	MCF-7	breast:	n/a	chr19:36157278-36157290
5	GATA3	chr19:36156971-36157572	MCF-7	breast:	n/a	n/a
6	NR2F2	chr19:36156956-36157593	MCF-7	breast:	n/a	n/a
7	ZNF217	chr19:36157098-36157341	MCF-7	breast:	n/a	n/a
8	POLR2A	chr19:36156962-36157563	ECC-1	luminal epithelium:	n/a	n/a
9	GATA3	chr19:36156829-36157534	MCF-7	breast:	n/a	n/a
10	FOXA1	chr19:36157152-36157350	T-47D	breast:	n/a	n/a
11	GATA3	chr19:36156990-36157388	MCF-7	breast:	n/a	n/a
12	TCF7L2	chr19:36157101-36157382	MCF-7	breast:	n/a	n/a
13	POLR2A	chr19:36156940-36157642	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr19:36156410-36157863	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr19:36156955-36157719	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr19:36157055-36157593	Hela-S3	cervix:	n/a	n/a
17	MAX	chr19:36156965-36157525	MCF-7	breast:	n/a	chr19:36157443-36157453
18	POLR2A	chr19:36157053-36157865	SK-N-MC	brain:	n/a	n/a
19	GATA3	chr19:36157070-36157411	T-47D	breast:	n/a	n/a
20	GATA3	chr19:36157012-36157434	T-47D	breast:	n/a	n/a
21	POLR2A	chr19:36157026-36157293	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
UPK1A	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs107068	0.82[LWK][hapmap]
rs12986089	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2242522	0.86[LWK][hapmap]
rs2285421	0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs231592	0.83[LWK][hapmap]
rs4806187	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61218414	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6510503	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv543995	chr19:36139204-36203592	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
6	nsv526166	chr19:36156588-36159368	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv817832	chr19:36156588-36159368	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
9	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs10422762	COX6B1	cis	Heart Left Ventricle	GTEx
rs10422762	COX6B1	trans	cerebellum	SCAN
rs10422762	UPK1A	trans	cerebellum	SCAN
rs10422762	ZBTB32	cis	Nerve Tibial	GTEx
rs10422762	COX6B1	cis	Muscle Skeletal	GTEx
rs10422762	FBXO27	cis	parietal	SCAN
rs10422762	UPK1A	cis	Adipose Subcutaneous	GTEx
rs10422762	ZBTB32	cis	lung	GTEx
rs10422762	COX6B1	trans	parietal	SCAN
rs10422762	RN7SL765P	cis	Muscle Skeletal	GTEx
rs10422762	ZNF780B	cis	cerebellum	SCAN
rs10422762	C19orf55	cis	Thyroid	GTEx
rs10422762	PHLDB3	cis	cerebellum	SCAN
rs10422762	LYPD4	cis	cerebellum	SCAN
rs10422762	UPK1A	cis	Esophagus Muscularis	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36140400-36164000	Weak transcription	Right Atrium	heart
2	chr19:36140600-36157200	Strong transcription	Fetal Stomach	stomach
3	chr19:36141400-36157200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr19:36142200-36157800	Weak transcription	Fetal Heart	heart
5	chr19:36142800-36157200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:36144600-36157200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr19:36144600-36157600	Strong transcription	Thymus	Thymus
8	chr19:36145800-36157200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr19:36149600-36158200	Weak transcription	Colon Smooth Muscle	Colon
10	chr19:36149600-36164000	Weak transcription	HMEC	breast
11	chr19:36149800-36157200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:36149800-36158000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:36149800-36158200	Weak transcription	NH-A	brain
14	chr19:36149800-36158400	Weak transcription	Fetal Brain Male	brain
15	chr19:36149800-36158400	Weak transcription	Small Intestine	intestine
16	chr19:36149800-36161600	Weak transcription	Osteobl	bone
17	chr19:36149800-36163400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:36150000-36158000	Weak transcription	Fetal Brain Female	brain
19	chr19:36150000-36160800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:36150200-36157600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr19:36151000-36157200	Weak transcription	HSMMtube	muscle
22	chr19:36151000-36158200	Weak transcription	Colonic Mucosa	Colon
23	chr19:36151000-36158400	Weak transcription	Fetal Intestine Large	intestine
24	chr19:36151200-36157200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr19:36151200-36157400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr19:36151200-36158000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr19:36151200-36158200	Weak transcription	NHEK	skin
28	chr19:36151200-36158400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:36151200-36158600	Weak transcription	Brain Germinal Matrix	brain
30	chr19:36151200-36158600	Weak transcription	NHLF	lung
31	chr19:36151200-36159200	Weak transcription	Ovary	ovary
32	chr19:36151200-36159200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr19:36151200-36159400	Weak transcription	A549	lung
34	chr19:36151200-36160800	Weak transcription	Brain Substantia Nigra	brain
35	chr19:36151200-36160800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr19:36152600-36158200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr19:36152600-36158200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:36152600-36158600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:36152600-36159800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr19:36152600-36160800	Weak transcription	Brain Hippocampus Middle	brain
41	chr19:36152600-36161000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr19:36152800-36162600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr19:36153000-36164000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr19:36153400-36160000	Weak transcription	HepG2	liver
45	chr19:36153600-36159600	Weak transcription	Primary B cells from cord blood	blood
46	chr19:36153800-36157600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr19:36153800-36157600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr19:36154200-36157600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr19:36154400-36157600	Weak transcription	Fetal Lung	lung
50	chr19:36154600-36157400	Strong transcription	Right Ventricle	heart

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