Variant report

Variant	rs10415370
Chromosome Location	chr19:36119289-36119290
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	chr19:36119207-36120217	MCF-7	breast:	n/a	n/a
2	GABPA	chr19:36119262-36120150	SK-N-SH	brain:	n/a	n/a
3	ZNF263	chr19:36119242-36120127	HEK293-T-REx	kidney:	n/a	n/a
4	PML	chr19:36119248-36120233	K562	blood:	n/a	n/a
5	POLR2A	chr19:36119262-36120199	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:36119281-36120618	MCF-7	breast:	n/a	n/a
7	BCL3	chr19:36119068-36120924	A549	lung:	n/a	chr19:36119646-36119655
8	GABPA	chr19:36119267-36120168	A549	lung:	n/a	n/a
9	SIN3AK20	chr19:36119289-36120181	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIX5	chr19:36119044-36120798	A549	lung:	n/a	n/a
11	POLR2A	chr19:36119180-36120157	U87	brain:	n/a	n/a
12	PAX5	chr19:36119275-36120084	GM12878	blood:	n/a	chr19:36119917-36119934
13	ETS1	chr19:36119198-36120194	A549	lung:	n/a	chr19:36119646-36119655 chr19:36119499-36119513 chr19:36119648-36119657 chr19:36119646-36119655 chr19:36119643-36119659 chr19:36119646-36119655 chr19:36119645-36119658 chr19:36119646-36119655 chr19:36119501-36119514
14	POLR2A	chr19:36119161-36120316	U87	brain:	n/a	n/a
15	ATF3	chr19:36119250-36120185	A549	lung:	n/a	chr19:36119652-36119661 chr19:36119913-36119933 chr19:36119911-36119924 chr19:36119914-36119922 chr19:36119911-36119922 chr19:36119946-36119966 chr19:36119947-36119958 chr19:36119914-36119921 chr19:36119910-36119925 chr19:36119913-36119921
16	POLR2A	chr19:36119233-36120220	PFSK-1	brain:	n/a	n/a
17	FOSL2	chr19:36119206-36120244	A549	lung:	n/a	chr19:36119913-36119922 chr19:36119849-36119858 chr19:36119887-36119896
18	E2F6	chr19:36119220-36120255	A549	lung:	n/a	chr19:36119914-36119923 chr19:36119912-36119921
19	MAX	chr19:36119120-36120431	A549	lung:	n/a	chr19:36120308-36120318
20	RFX5	chr19:36119108-36120787	IMR90	lung:	n/a	chr19:36119888-36119897 chr19:36119850-36119859
21	ELF1	chr19:36119274-36120266	MCF-7	breast:	n/a	chr19:36119654-36119666
22	POLR2A	chr19:36119245-36120777	HL-60	blood:	n/a	n/a
23	GABPA	chr19:36119206-36120349	MCF-7	breast:	n/a	chr19:36120310-36120319
24	PML	chr19:36119043-36120316	GM12878	blood:	n/a	n/a
25	MAX	chr19:36119134-36120326	A549	lung:	n/a	chr19:36120308-36120318
26	ELF1	chr19:36119279-36120135	K562	blood:	n/a	chr19:36119654-36119666
27	CEBPB	chr19:36119232-36120185	A549	lung:	n/a	chr19:36119889-36119897
28	NR2F2	chr19:36119252-36120104	K562	blood:	n/a	n/a
29	POLR2A	chr19:36119256-36120231	GM12891	blood:	n/a	n/a
30	POLR2A	chr19:36119173-36120316	U87	brain:	n/a	n/a
31	YY1	chr19:36119280-36120340	K562	blood:	n/a	chr19:36120310-36120319
32	POLR2A	chr19:36119247-36120675	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr19:36119252-36119832	GM12891	blood:	n/a	n/a
34	POLR2A	chr19:36119222-36120280	GM12878	blood:	n/a	n/a
35	POLR2A	chr19:36119238-36120598	GM12892	blood:	n/a	n/a
36	TCF12	chr19:36119096-36120836	A549	lung:	n/a	n/a
37	GATA3	chr19:36119123-36120394	A549	lung:	n/a	chr19:36120316-36120325
38	POLR2A	chr19:36119262-36120229	ECC-1	luminal epithelium:	n/a	n/a
39	JUN	chr19:36119153-36120272	K562	blood:	n/a	chr19:36119913-36119922 chr19:36119909-36119922 chr19:36119849-36119858 chr19:36119887-36119896
40	SIN3AK20	chr19:36119200-36120360	MCF-7	breast:	n/a	n/a
41	EP300	chr19:36119255-36120253	A549	lung:	n/a	chr19:36119647-36119654
42	POLR2A	chr19:36119255-36120711	PBDE	blood:	n/a	n/a
43	POLR2A	chr19:36119150-36120822	H1-hESC	embryonic stem cell:	n/a	n/a
44	ELF1	chr19:36119174-36120143	A549	lung:	n/a	chr19:36119654-36119666
45	ELF1	chr19:36119275-36120243	MCF-7	breast:	n/a	chr19:36119654-36119666
46	POLR2A	chr19:36119110-36120402	K562	blood:	n/a	n/a
47	RFX5	chr19:36119152-36120554	SK-N-SH	brain:	n/a	chr19:36119888-36119897 chr19:36119850-36119859
48	POLR2A	chr19:36119237-36120214	GM12891	blood:	n/a	n/a
49	POLR2A	chr19:36119285-36120169	K562	blood:	n/a	n/a
50	HCFC1	chr19:36119136-36120802	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36118103..36121861-chr19:36131558..36136331,8	MCF-7	breast:
2	chr19:35739540..35741218-chr19:36118965..36121902,2	MCF-7	breast:
3	chr19:36034987..36038890-chr19:36118307..36121069,4	MCF-7	breast:
4	chr19:36053526..36055701-chr19:36117246..36119679,2	MCF-7	breast:
5	chr19:35756917..35760158-chr19:36118192..36121519,3	K562	blood:
6	chr19:36118147..36121531-chr19:36133247..36136800,5	MCF-7	breast:
7	chr19:36102107..36105519-chr19:36117943..36120957,6	MCF-7	breast:
8	chr19:36114642..36116458-chr19:36117906..36119551,2	MCF-7	breast:
9	chr19:36102330..36105424-chr19:36117998..36119603,3	MCF-7	breast:
10	chr19:36118444..36125285-chr19:36125367..36133017,11	MCF-7	breast:
11	chr19:36118346..36121729-chr19:36137061..36140850,4	MCF-7	breast:

Variant related genes	Relation type
RBM42	TF binding region
ENSG00000105677	Chromatin interaction
ENSG00000236144	Chromatin interaction
ENSG00000105698	Chromatin interaction
ENSG00000105675	Chromatin interaction
ENSG00000249115	Chromatin interaction
ENSG00000105699	Chromatin interaction
ENSG00000105672	Chromatin interaction
ENSG00000126267	Chromatin interaction
ENSG00000267626	Chromatin interaction

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

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

rs_ID	r²[population]
rs10403109	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10418323	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10418680	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10420252	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10420286	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs12459935	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs1544332	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2267585	0.91[JPT][hapmap]
rs2285419	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2311873	0.85[CEU][hapmap]
rs57405530	0.80[EUR][1000 genomes]
rs57411749	0.80[EUR][1000 genomes]
rs6510502	1.00[CEU][hapmap]
rs7249516	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[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	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	esv2599797	chr19:36117682-36119524	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 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	chr19:36113000-36119400	Weak transcription	Spleen	Spleen
2	chr19:36118800-36119400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr19:36118800-36119600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:36118800-36119600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr19:36118800-36120800	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr19:36119000-36119400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:36119000-36119400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr19:36119000-36119400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr19:36119000-36119400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
10	chr19:36119000-36119400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr19:36119000-36119400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr19:36119000-36119400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:36119000-36119400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:36119000-36119400	Flanking Active TSS	Brain Angular Gyrus	brain
15	chr19:36119000-36119400	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr19:36119000-36119400	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr19:36119000-36119400	Flanking Active TSS	Fetal Heart	heart
18	chr19:36119000-36119400	Flanking Active TSS	Fetal Lung	lung
19	chr19:36119000-36119400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr19:36119000-36119400	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr19:36119000-36119400	Flanking Active TSS	Thymus	Thymus
22	chr19:36119000-36119400	Flanking Active TSS	Hela-S3	cervix
23	chr19:36119000-36119400	Active TSS	HepG2	liver
24	chr19:36119000-36119400	Flanking Active TSS	HMEC	breast
25	chr19:36119000-36119400	Flanking Active TSS	HSMMtube	muscle
26	chr19:36119000-36119400	Flanking Active TSS	NHLF	lung
27	chr19:36119000-36119400	Flanking Active TSS	Osteobl	bone
28	chr19:36119000-36119600	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr19:36119000-36119600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr19:36119000-36119600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr19:36119000-36119600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr19:36119000-36119600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr19:36119000-36119600	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr19:36119000-36119600	Flanking Active TSS	Fetal Muscle Trunk	muscle
35	chr19:36119000-36119600	Flanking Active TSS	Dnd41	blood
36	chr19:36119000-36119600	Flanking Active TSS	HUVEC	blood vessel
37	chr19:36119000-36119600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr19:36119000-36119800	Active TSS	Right Atrium	heart
39	chr19:36119000-36120000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:36119000-36120200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:36119000-36120400	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr19:36119000-36120400	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr19:36119000-36120400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:36119000-36120400	Active TSS	Muscle Satellite Cultured Cells	--
45	chr19:36119000-36120400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr19:36119000-36120400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:36119000-36120400	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr19:36119000-36120400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr19:36119000-36120400	Active TSS	Brain Substantia Nigra	brain
50	chr19:36119000-36120400	Active TSS	Colonic Mucosa	Colon

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