Variant report

Variant	rs10415973
Chromosome Location	chr19:41303668-41303669
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	SMC3	chr19:41303553-41304662	HepG2	liver:	n/a	chr19:41304144-41304158
2	TCF12	chr19:41303652-41306370	A549	lung:	n/a	chr19:41304331-41304341 chr19:41305722-41305732 chr19:41304332-41304339 chr19:41306069-41306076
3	CTCF	chr19:41303560-41303710	WI-38	lung:	n/a	n/a
4	POLR2A	chr19:41303426-41303722	K562	blood:	n/a	n/a
5	MXI1	chr19:41303661-41306345	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr19:41303617-41305677	HepG2	liver:	n/a	n/a
7	WRNIP1	chr19:41303629-41304709	GM12878	blood:	n/a	n/a
8	MAX	chr19:41303632-41306288	A549	lung:	n/a	chr19:41305045-41305054 chr19:41305044-41305055 chr19:41304746-41304756 chr19:41305810-41305820
9	MXI1	chr19:41303457-41305285	HepG2	liver:	n/a	n/a
10	JUND	chr19:41303450-41303737	HepG2	liver:	n/a	chr19:41303625-41303635 chr19:41303625-41303635 chr19:41303624-41303635 chr19:41303625-41303635
11	SIX5	chr19:41303632-41304919	A549	lung:	n/a	n/a
12	MTA3	chr19:41303177-41305106	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:41303613-41305743	GM19193	blood:	n/a	n/a
14	MAX	chr19:41303630-41305333	HCT-116	colon:	n/a	chr19:41305045-41305054 chr19:41305044-41305055 chr19:41304746-41304756
15	MAX	chr19:41303174-41305773	HepG2	liver:	n/a	chr19:41305045-41305054 chr19:41303294-41303303 chr19:41305044-41305055 chr19:41304746-41304756
16	BCL3	chr19:41303597-41305311	A549	lung:	n/a	chr19:41304894-41304903
17	ARID3A	chr19:41303469-41305052	HepG2	liver:	n/a	n/a
18	FOSL2	chr19:41303394-41303763	HepG2	liver:	n/a	chr19:41303625-41303635 chr19:41303625-41303635 chr19:41303625-41303635
19	CREB1	chr19:41303457-41305864	HepG2	liver:	n/a	n/a
20	STAT5A	chr19:41303663-41304959	GM12878	blood:	n/a	chr19:41304383-41304394 chr19:41304890-41304902 chr19:41304079-41304087
21	HCFC1	chr19:41303538-41305891	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41280731..41296556-chr19:41299561..41307605,30	MCF-7	breast:
2	chr19:41254487..41259247-chr19:41302579..41309995,18	K562	blood:
3	chr19:41296534..41298700-chr19:41301407..41304714,3	K562	blood:
4	chr19:41303367..41304323-chr22:38709262..38710196,2	Hela-S3	cervix:
5	chr19:41281732..41286442-chr19:41302482..41306628,13	K562	blood:
6	chr19:41303143..41305588-chr19:41428304..41431722,3	MCF-7	breast:
7	chr19:41254747..41256268-chr19:41303480..41305851,2	MCF-7	breast:
8	chr19:41281718..41286533-chr19:41301356..41311124,20	K562	blood:
9	chr19:41221300..41223743-chr19:41303378..41306610,3	MCF-7	breast:
10	chr19:41168344..41169236-chr19:41303602..41304477,3	K562	blood:
11	chr19:41253776..41259894-chr19:41301950..41310086,19	MCF-7	breast:
12	chr19:41220238..41223312-chr19:41303618..41307521,4	K562	blood:
13	chr19:41224721..41227148-chr19:41302837..41304471,2	K562	blood:
14	chr19:41253887..41263110-chr19:41303366..41316425,33	K562	blood:
15	chr19:41220057..41225402-chr19:41302090..41307926,9	MCF-7	breast:

Variant related genes	Relation type
EGLN2	TF binding region
ENSG00000268797	TF binding region
ENSG00000256612	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000123815	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10402565	1.00[AMR][1000 genomes]
rs10405792	1.00[AMR][1000 genomes]
rs10408452	1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10417139	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420158	1.00[AMR][1000 genomes]
rs10422737	1.00[AMR][1000 genomes]
rs11083594	1.00[AMR][1000 genomes]
rs12104289	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs13345967	1.00[AMR][1000 genomes]
rs13347002	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28368968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28609092	1.00[AMR][1000 genomes]
rs28636772	1.00[AMR][1000 genomes]

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	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41285000-41303800	Weak transcription	Small Intestine	intestine
2	chr19:41285000-41304000	Weak transcription	Psoas Muscle	Psoas
3	chr19:41285200-41303800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr19:41285200-41304000	Weak transcription	HSMM	muscle
5	chr19:41285400-41303800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr19:41285400-41303800	Weak transcription	NH-A	brain
7	chr19:41285400-41304000	Weak transcription	HSMMtube	muscle
8	chr19:41286200-41303800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr19:41286200-41304000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:41286400-41303800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:41293000-41303800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr19:41293000-41304000	Weak transcription	Brain Angular Gyrus	brain
13	chr19:41293000-41304000	Weak transcription	Brain Substantia Nigra	brain
14	chr19:41293200-41303800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr19:41296200-41303800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:41296200-41304000	Weak transcription	Right Ventricle	heart
17	chr19:41297600-41303800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr19:41297600-41304000	Weak transcription	Gastric	stomach
19	chr19:41298000-41304000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr19:41298200-41303800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr19:41298200-41303800	Weak transcription	Brain Germinal Matrix	brain
22	chr19:41298200-41304000	Weak transcription	Right Atrium	heart
23	chr19:41298400-41303800	Weak transcription	Fetal Muscle Leg	muscle
24	chr19:41298400-41304000	Weak transcription	Fetal Brain Female	brain
25	chr19:41298600-41303800	Weak transcription	Brain Anterior Caudate	brain
26	chr19:41298600-41303800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr19:41298600-41303800	Weak transcription	Brain Hippocampus Middle	brain
28	chr19:41298600-41304000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr19:41298600-41304000	Weak transcription	Primary T cells from cord blood	blood
30	chr19:41298600-41304000	Weak transcription	Fetal Kidney	kidney
31	chr19:41298800-41304000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:41299000-41303800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:41299200-41303800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:41299200-41303800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr19:41299200-41303800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:41299200-41303800	Weak transcription	Stomach Mucosa	stomach
37	chr19:41302200-41304000	Genic enhancers	Primary B cells from peripheral blood	blood
38	chr19:41302800-41304000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr19:41303000-41303800	Weak transcription	Fetal Stomach	stomach
40	chr19:41303000-41304000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr19:41303200-41303800	Genic enhancers	Primary B cells from cord blood	blood
42	chr19:41303200-41303800	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr19:41303200-41303800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:41303200-41303800	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr19:41303200-41304000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:41303200-41304000	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr19:41303200-41304400	Enhancers	Spleen	Spleen
48	chr19:41303400-41303800	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr19:41303400-41303800	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr19:41303400-41303800	Enhancers	Primary T helper cells PMA-I stimulated	--

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