Variant report

Variant	rs59417293
Chromosome Location	chr7:104650519-104650520
allele	A/C
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	chr7:104649871-104658724	K562	blood:	n/a	n/a
2	TCF7L2	chr7:104650230-104650921	HEK293	kidney:	n/a	chr7:104650554-104650568 chr7:104650554-104650568 chr7:104650557-104650566
3	POLR2A	chr7:104650500-104651456	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:104650139-104656413	GM12878	blood:	n/a	n/a
5	POLR2A	chr7:104649793-104655808	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr7:104650238-104656311	GM12891	blood:	n/a	n/a
7	POLR2A	chr7:104650113-104654922	HepG2	liver:	n/a	n/a
8	POLR2A	chr7:104650286-104655760	HUVEC	blood vessel:	n/a	n/a
9	IRF1	chr7:104650448-104656728	K562	blood:	n/a	chr7:104652192-104652212 chr7:104653598-104653607 chr7:104656077-104656087 chr7:104651485-104651498 chr7:104652632-104652642 chr7:104653674-104653687 chr7:104652628-104652642 chr7:104651982-104651994
10	POLR2A	chr7:104649851-104650574	K562	blood:	n/a	n/a
11	TCF7L2	chr7:104650470-104650654	MCF-7	breast:	n/a	chr7:104650554-104650568 chr7:104650554-104650568 chr7:104650557-104650566
12	MXI1	chr7:104649971-104659449	SK-N-SH	brain:	n/a	n/a
13	CHD1	chr7:104650096-104658695	IMR90	lung:	n/a	n/a
14	POLR2A	chr7:104650231-104656216	GM12878	blood:	n/a	n/a
15	MXI1	chr7:104650193-104650525	GM12878	blood:	n/a	n/a
16	POLR2A	chr7:104650339-104656433	IMR90	lung:	n/a	n/a
17	POLR2A	chr7:104650482-104650971	Hela-S3	cervix:	n/a	n/a
18	GATA3	chr7:104650518-104650636	SH-SY5Y	brain:	n/a	n/a
19	POLR2A	chr7:104650440-104656270	HepG2	liver:	n/a	n/a
20	WRNIP1	chr7:104650169-104651495	GM12878	blood:	n/a	n/a
21	GATA2	chr7:104650411-104650657	SH-SY5Y	brain:	n/a	n/a
22	POLR2A	chr7:104649911-104656477	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr7:104649959-104656247	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr7:104650360-104651247	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr7:104650408-104651170	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:72476582..72478189-chr7:104650247..104653086,2	MCF-7	breast:
2	chr7:104592455..104594379-chr7:104649567..104651411,2	K562	blood:
3	chr7:104649355..104651089-chr7:105173782..105176536,2	K562	blood:
4	chr7:104649613..104651128-chr7:104876520..104878391,2	K562	blood:
5	chr7:104647926..104656528-chr7:104691112..104706949,31	K562	blood:
6	chr7:104649592..104657753-chr7:104694428..104703365,16	MCF-7	breast:
7	chr7:104649601..104653676-chr7:105029497..105032094,4	K562	blood:
8	chr7:104650505..104654814-chr7:104745765..104750461,6	K562	blood:
9	chr7:104648889..104654837-chr7:104768923..104775807,9	K562	blood:
10	chr7:104585890..104587926-chr7:104648432..104650554,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRPK2-1	chr7:104637584-104654636	NONHSAT122594

Variant related genes	Relation type
KMT2E	TF binding region
ENSG00000272918	Chromatin interaction
ENSG00000135250	Chromatin interaction
ENSG00000005483	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12111884	1.00[EUR][1000 genomes]
rs2299302	1.00[EUR][1000 genomes]
rs28588491	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28832590	1.00[EUR][1000 genomes]
rs55931372	1.00[EUR][1000 genomes]
rs57280586	1.00[EUR][1000 genomes]
rs59691189	1.00[EUR][1000 genomes]
rs60188077	1.00[EUR][1000 genomes]
rs60766560	1.00[EUR][1000 genomes]
rs73404021	1.00[EUR][1000 genomes]
rs73715438	1.00[EUR][1000 genomes]
rs73715439	1.00[EUR][1000 genomes]
rs73716467	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73717957	1.00[EUR][1000 genomes]
rs73717959	1.00[EUR][1000 genomes]
rs73717961	1.00[EUR][1000 genomes]
rs73717963	1.00[EUR][1000 genomes]
rs73718220	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs757957	1.00[EUR][1000 genomes]

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	nsv1029283	chr7:104571741-104729168	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	132 gene(s)	inside rSNPs	diseases
2	nsv888927	chr7:104614664-104781644	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
3	esv2829879	chr7:104618318-104652671	Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv608068	chr7:104622402-104757483	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104641800-104651800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:104642000-104650600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:104642400-104651000	Weak transcription	Esophagus	oesophagus
4	chr7:104642400-104652200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:104643600-104650800	Genic enhancers	Primary B cells from peripheral blood	blood
6	chr7:104646400-104651000	Weak transcription	Lung	lung
7	chr7:104646800-104651000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr7:104647000-104650800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr7:104647400-104650600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:104647800-104650800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:104648200-104650600	Enhancers	Fetal Brain Male	brain
12	chr7:104648400-104650800	Weak transcription	Gastric	stomach
13	chr7:104648400-104650800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
14	chr7:104648400-104651800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:104648400-104651800	Weak transcription	Pancreas	Pancrea
16	chr7:104648600-104652000	Transcr. at gene 5' and 3'	Dnd41	blood
17	chr7:104648600-104658800	Active TSS	Ovary	ovary
18	chr7:104648800-104651600	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr7:104649000-104650600	Enhancers	Primary hematopoietic stem cells	blood
20	chr7:104649000-104650800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr7:104649000-104652800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr7:104649000-104657400	Active TSS	Colonic Mucosa	Colon
23	chr7:104649200-104651800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr7:104649200-104652000	Transcr. at gene 5' and 3'	K562	blood
25	chr7:104649200-104652200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr7:104649200-104653000	Active TSS	Right Atrium	heart
27	chr7:104649200-104659000	Active TSS	Right Ventricle	heart
28	chr7:104649400-104650600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr7:104649400-104650600	Active TSS	Brain Germinal Matrix	brain
30	chr7:104649400-104650600	Flanking Active TSS	HUVEC	blood vessel
31	chr7:104649400-104650800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr7:104649400-104650800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr7:104649400-104650800	Weak transcription	Stomach Mucosa	stomach
34	chr7:104649400-104651600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr7:104649400-104651600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr7:104649400-104651800	Weak transcription	Spleen	Spleen
37	chr7:104649400-104652000	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr7:104649400-104652600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr7:104649400-104652600	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr7:104649400-104656800	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr7:104649400-104658800	Active TSS	Aorta	Aorta
42	chr7:104649400-104659400	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr7:104649600-104650600	Enhancers	Liver	Liver
44	chr7:104649600-104650600	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr7:104649600-104650600	Active TSS	NHDF-Ad	bronchial
46	chr7:104649600-104651000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr7:104649600-104651200	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr7:104649600-104651600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr7:104649600-104653200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr7:104649600-104657000	Active TSS	Colon Smooth Muscle	Colon

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