Variant report

Variant	rs10416308
Chromosome Location	chr19:41312261-41312262
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41312161-41313531	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr19:41311386-41318263	K562	blood:	n/a	n/a
3	POLR2A	chr19:41312192-41313213	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr19:41311568-41312668	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr19:41311611-41314969	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr19:41312191-41312384	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:41312187-41313598	HL-60	blood:	n/a	n/a
8	POLR2A	chr19:41312123-41316155	GM12892	blood:	n/a	n/a
9	TCF12	chr19:41312237-41314213	A549	lung:	n/a	chr19:41313460-41313470
10	POLR2A	chr19:41311961-41317444	GM12891	blood:	n/a	n/a
11	MAZ	chr19:41311984-41313308	IMR90	lung:	n/a	n/a
12	POLR2A	chr19:41312066-41318528	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:41308880-41317807	GM12891	blood:	n/a	n/a
14	POLR2A	chr19:41309752-41318497	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr19:41308407-41313533	K562	blood:	n/a	n/a
16	POLR2A	chr19:41307117-41318353	K562	blood:	n/a	n/a
17	CHD1	chr19:41311939-41313480	IMR90	lung:	n/a	n/a
18	POLR2A	chr19:41307663-41316128	GM12892	blood:	n/a	n/a
19	POLR2A	chr19:41311543-41313529	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr19:41312223-41314188	SK-N-SH	brain:	n/a	n/a
21	MXI1	chr19:41311936-41313300	IMR90	lung:	n/a	n/a
22	POLR2A	chr19:41312165-41313954	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr19:41312247-41313241	H1-neurons	neurons:	n/a	n/a
24	POLR2A	chr19:41307781-41314972	GM12891	blood:	n/a	n/a
25	BCL3	chr19:41311885-41314853	A549	lung:	n/a	n/a
26	JUND	chr19:41311881-41314263	SK-N-SH	brain:	n/a	chr19:41313678-41313688 chr19:41313678-41313688 chr19:41313678-41313687 chr19:41313680-41313691 chr19:41313679-41313688 chr19:41313677-41313688 chr19:41313677-41313689 chr19:41313679-41313686
27	POLR2A	chr19:41309515-41312290	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:41312168-41317364	GM12892	blood:	n/a	n/a
29	POLR2A	chr19:41312222-41313169	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr19:41308432-41316432	K562	blood:	n/a	n/a
31	SIX5	chr19:41312112-41313765	A549	lung:	n/a	n/a
32	POLR2A	chr19:41307640-41313313	K562	blood:	n/a	n/a
33	POLR2A	chr19:41312232-41313367	H1-neurons	neurons:	n/a	n/a
34	POLR2A	chr19:41308985-41316368	A549	lung:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41282306..41285368-chr19:41311943..41315414,5	MCF-7	breast:
2	chr19:41253320..41258890-chr19:41311950..41315573,6	MCF-7	breast:
3	chr19:41221142..41224353-chr19:41311383..41314668,3	K562	blood:
4	chr19:41310513..41314653-chr19:41415794..41419669,4	K562	blood:
5	chr19:41223813..41226637-chr19:41310296..41313871,3	MCF-7	breast:
6	chr19:41267484..41269645-chr19:41312151..41314875,2	K562	blood:
7	chr19:41280805..41286068-chr19:41308324..41316733,13	K562	blood:
8	chr19:41254272..41257133-chr19:41310784..41312768,2	MCF-7	breast:
9	chr19:41195260..41197933-chr19:41310864..41312582,2	K562	blood:
10	chr19:41220938..41225137-chr19:41311275..41314518,5	K562	blood:
11	chr19:41220720..41224635-chr19:41312175..41316788,5	MCF-7	breast:
12	chr19:41253887..41263110-chr19:41303366..41316425,33	K562	blood:
13	chr19:41282175..41285758-chr19:41311471..41315456,8	K562	blood:
14	chr19:41221436..41223725-chr19:41310201..41314445,5	MCF-7	breast:

No data

Variant related genes	Relation type
EGLN2	TF binding region
ENSG00000261857	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000198251	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000188493	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10403040	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10405596	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10405633	0.82[EUR][1000 genomes]
rs10411008	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10413760	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10423139	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11083567	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11083568	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11881124	0.84[ASN][1000 genomes]
rs2287691	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28660501	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3875144	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56101381	0.82[EUR][1000 genomes]
rs8113056	0.83[AFR][1000 genomes];0.89[ASN][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	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
4	nsv1066637	chr19:41309211-41597896	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS 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	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41305800-41316200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:41306200-41313200	Enhancers	Fetal Heart	heart
3	chr19:41306400-41313600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr19:41306400-41313800	Genic enhancers	Fetal Thymus	thymus
5	chr19:41306400-41316200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr19:41306400-41316800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr19:41306600-41312400	Genic enhancers	Fetal Muscle Trunk	muscle
8	chr19:41306600-41314000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:41306600-41314800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr19:41306800-41313400	Genic enhancers	Gastric	stomach
11	chr19:41307000-41312400	Enhancers	Small Intestine	intestine
12	chr19:41307000-41313400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
13	chr19:41307000-41315800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:41307200-41312400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
15	chr19:41308000-41313600	Weak transcription	Aorta	Aorta
16	chr19:41308200-41313200	Enhancers	Liver	Liver
17	chr19:41308200-41313400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr19:41308400-41313600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:41308400-41313600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:41308400-41316400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr19:41308600-41313600	Enhancers	Psoas Muscle	Psoas
22	chr19:41308800-41312400	Enhancers	Brain Substantia Nigra	brain
23	chr19:41308800-41313200	Enhancers	Pancreas	Pancrea
24	chr19:41308800-41313400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:41308800-41313400	Genic enhancers	Fetal Intestine Large	intestine
26	chr19:41308800-41313600	Enhancers	Fetal Brain Male	brain
27	chr19:41308800-41313800	Genic enhancers	A549	lung
28	chr19:41308800-41314000	Genic enhancers	Esophagus	oesophagus
29	chr19:41309000-41312600	Enhancers	Stomach Mucosa	stomach
30	chr19:41309000-41313800	Genic enhancers	Fetal Muscle Leg	muscle
31	chr19:41309000-41316200	Genic enhancers	Placenta	Placenta
32	chr19:41309200-41312400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:41309200-41312400	Genic enhancers	NHLF	lung
34	chr19:41309200-41313200	Genic enhancers	Primary monocytes fromperipheralblood	blood
35	chr19:41309200-41313600	Enhancers	Right Atrium	heart
36	chr19:41309200-41314200	Genic enhancers	Fetal Stomach	stomach
37	chr19:41309200-41315600	Genic enhancers	Right Ventricle	heart
38	chr19:41309400-41316000	Genic enhancers	Spleen	Spleen
39	chr19:41309600-41312400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr19:41309600-41313000	Enhancers	Left Ventricle	heart
41	chr19:41309800-41313000	Genic enhancers	K562	blood
42	chr19:41309800-41313600	Genic enhancers	Fetal Intestine Small	intestine
43	chr19:41309800-41313600	Genic enhancers	Rectal Mucosa Donor 31	rectum
44	chr19:41309800-41313800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr19:41309800-41316200	Genic enhancers	Lung	lung
46	chr19:41309800-41316400	Genic enhancers	Primary B cells from peripheral blood	blood
47	chr19:41310000-41315200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
48	chr19:41310200-41313000	Enhancers	Colonic Mucosa	Colon
49	chr19:41310400-41312600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr19:41310400-41313200	Enhancers	H1 Cell Line	embryonic stem cell

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