Variant report

Variant	rs3750669
Chromosome Location	chr10:6131029-6131030
allele	G/T
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	YY1	chr10:6130682-6131328	K562	blood:	n/a	chr10:6131052-6131061 chr10:6130865-6130874 chr10:6131171-6131185 chr10:6131168-6131179 chr10:6131015-6131024
2	POLR2A	chr10:6130700-6131848	Raji	blood:	n/a	n/a
3	SP1	chr10:6130517-6131064	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr10:6130732-6131748	MCF-7	breast:	n/a	n/a
5	JUN	chr10:6130655-6131032	K562	blood:	n/a	chr10:6130744-6130758
6	MAZ	chr10:6130633-6131162	HepG2	liver:	n/a	n/a
7	STAT5A	chr10:6130572-6131074	K562	blood:	n/a	n/a
8	CTCF	chr10:6130613-6131060	Gliobla	brain:	n/a	n/a
9	CTCF	chr10:6130288-6132114	SK-N-SH	brain:	n/a	chr10:6131172-6131185 chr10:6131800-6131813 chr10:6131176-6131185 chr10:6131066-6131079
10	YY1	chr10:6130535-6131394	GM12878	blood:	n/a	chr10:6131052-6131061 chr10:6131360-6131374 chr10:6131365-6131374 chr10:6130865-6130874 chr10:6131171-6131185 chr10:6131168-6131179 chr10:6131362-6131371 chr10:6131015-6131024
11	SIN3AK20	chr10:6130642-6131316	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr10:6130867-6131147	GM12892	blood:	n/a	n/a
13	MBD4	chr10:6130631-6131051	HepG2	liver:	n/a	n/a
14	POLR2A	chr10:6130747-6131811	IMR90	lung:	n/a	n/a
15	NRF1	chr10:6130807-6131100	HepG2	liver:	n/a	chr10:6130951-6130962 chr10:6130968-6130979 chr10:6130927-6130938
16	POLR2A	chr10:6130847-6131324	GM12878	blood:	n/a	n/a
17	MAX	chr10:6130514-6131151	A549	lung:	n/a	n/a
18	MAX	chr10:6130567-6132097	K562	blood:	n/a	n/a
19	POLR2A	chr10:6130832-6131316	GM12892	blood:	n/a	n/a
20	ZEB1	chr10:6130631-6131053	GM12878	blood:	n/a	n/a
21	E2F6	chr10:6130752-6131329	K562	blood:	n/a	chr10:6131015-6131024 chr10:6131117-6131126
22	RCOR1	chr10:6130611-6131148	GM12878	blood:	n/a	n/a
23	CTCF	chr10:6130325-6131122	MCF-7	breast:	n/a	chr10:6131066-6131079
24	TEAD4	chr10:6130549-6131064	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr10:6129833-6132689	A549	lung:	n/a	chr10:6131172-6131185 chr10:6132605-6132618 chr10:6131800-6131813 chr10:6131176-6131185 chr10:6131066-6131079
26	TAF1	chr10:6130734-6131398	HepG2	liver:	n/a	n/a
27	CTCF	chr10:6130671-6131032	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr10:6130816-6131256	HL-60	blood:	n/a	n/a
29	TBP	chr10:6130660-6131232	K562	blood:	n/a	n/a
30	TAF1	chr10:6130561-6131272	ECC-1	luminal epithelium:	n/a	n/a
31	TCF12	chr10:6130494-6131148	A549	lung:	n/a	n/a
32	BCLAF1	chr10:6130507-6131438	GM12878	blood:	n/a	chr10:6131015-6131028 chr10:6131315-6131328 chr10:6131361-6131374 chr10:6131067-6131080 chr10:6130719-6130728 chr10:6131364-6131373 chr10:6131265-6131274 chr10:6131358-6131371
33	IRF1	chr10:6130616-6131147	K562	blood:	n/a	n/a
34	TEAD4	chr10:6130555-6131132	A549	lung:	n/a	n/a
35	CHD2	chr10:6130640-6131325	GM12878	blood:	n/a	n/a
36	POLR2A	chr10:6130732-6131581	K562	blood:	n/a	n/a
37	ZBTB33	chr10:6130670-6131031	A549	lung:	n/a	n/a
38	POLR2A	chr10:6130817-6132126	GM12878	blood:	n/a	n/a
39	PML	chr10:6130651-6131118	GM12878	blood:	n/a	n/a
40	TCF12	chr10:6130628-6131182	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr10:6130738-6131346	GM12878	blood:	n/a	n/a
42	CTCF	chr10:6130533-6131120	ECC-1	luminal epithelium:	n/a	chr10:6131066-6131079
43	TAF1	chr10:6130592-6131443	ECC-1	luminal epithelium:	n/a	n/a
44	CTCF	chr10:6130652-6131057	Pancreas_OC	pancreas:	n/a	n/a
45	ATF3	chr10:6130673-6131086	GM12878	blood:	n/a	chr10:6131013-6131022
46	CTCF	chr10:6130599-6131048	GM12878	blood:	n/a	n/a
47	FOXA2	chr10:6130701-6131203	A549	lung:	n/a	n/a
48	POLR2A	chr10:6130875-6131160	HepG2	liver:	n/a	n/a
49	CTCF	chr10:6130625-6131086	GM19238	blood:	n/a	chr10:6131066-6131079
50	POLR2A	chr10:6130746-6131835	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:6130789..6132928-chr10:6134999..6139816,5	MCF-7	breast:
2	chr10:6128377..6132115-chr10:6241834..6247197,6	MCF-7	breast:
3	chr10:6129764..6131854-chr10:6149478..6152087,2	MCF-7	breast:
4	chr10:6018551..6021640-chr10:6130714..6134315,5	MCF-7	breast:
5	chr10:6018064..6019912-chr10:6129955..6132156,2	K562	blood:
6	chr10:6130483..6131187-chr17:58513324..58513942,2	MCF-7	breast:
7	chr10:6130983..6133585-chr10:6620139..6622430,2	K562	blood:
8	chr10:6129825..6133257-chr10:6241985..6247329,10	MCF-7	breast:
9	chr10:6018278..6019533-chr10:6130531..6131243,3	MCF-7	breast:
10	chr10:6130591..6133050-chr10:6185385..6187497,2	MCF-7	breast:
11	chr10:6018064..6021783-chr10:6129304..6132316,4	K562	blood:
12	chr10:6019647..6020148-chr10:6130484..6131213,2	MCF-7	breast:
13	chr10:6129204..6131748-chr10:6244207..6246414,2	K562	blood:
14	chr10:6130589..6132639-chr10:6184439..6189476,5	K562	blood:
15	chr10:6130957..6132763-chr10:6153390..6155892,2	MCF-7	breast:

Variant related genes	Relation type
RBM17	TF binding region
ENSG00000134470	Chromatin interaction
ENSG00000237943	Chromatin interaction
ENSG00000170525	Chromatin interaction
ENSG00000213994	Chromatin interaction
ENSG00000134453	Chromatin interaction
ENSG00000213228	Chromatin interaction
ENSG00000065675	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11256664	0.89[ASN][1000 genomes]
rs11256685	0.89[ASN][1000 genomes]
rs11256761	0.89[ASN][1000 genomes]
rs11256763	0.81[ASN][1000 genomes]
rs11256801	0.89[ASN][1000 genomes]
rs11256810	0.89[ASN][1000 genomes]
rs11256854	0.81[ASN][1000 genomes]
rs12252274	0.89[ASN][1000 genomes]
rs12254328	0.85[ASN][1000 genomes]
rs12262454	0.89[ASN][1000 genomes]
rs12263912	0.89[ASN][1000 genomes]
rs12264240	0.89[ASN][1000 genomes]
rs12416306	0.89[ASN][1000 genomes]
rs58138632	0.89[ASN][1000 genomes]
rs59330649	0.89[ASN][1000 genomes]
rs60859211	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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	76 gene(s)	inside rSNPs	diseases
3	nsv894815	chr10:6108439-6161781	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1040397	chr10:6129759-6158697	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv3410151	chr10:6129771-6132319	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6129000-6131200	Weak transcription	Placenta	Placenta
2	chr10:6129000-6131400	Weak transcription	Fetal Heart	heart
3	chr10:6130200-6132000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr10:6130400-6131200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr10:6130400-6131200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr10:6130400-6131200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr10:6130400-6131400	Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr10:6130400-6131600	Active TSS	Brain Anterior Caudate	brain
9	chr10:6130400-6131600	Active TSS	Fetal Muscle Trunk	muscle
10	chr10:6130400-6131600	Active TSS	Stomach Smooth Muscle	stomach
11	chr10:6130400-6131800	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr10:6130400-6131800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr10:6130400-6131800	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr10:6130400-6131800	Active TSS	NHEK	skin
15	chr10:6130400-6132000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:6130400-6132000	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr10:6130400-6132000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr10:6130400-6132000	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr10:6130400-6132000	Active TSS	Fetal Lung	lung
20	chr10:6130400-6132000	Active TSS	K562	blood
21	chr10:6130400-6132000	Active TSS	NH-A	brain
22	chr10:6130400-6132000	Active TSS	NHDF-Ad	bronchial
23	chr10:6130400-6132000	Active TSS	NHLF	lung
24	chr10:6130400-6132200	Active TSS	H1 Cell Line	embryonic stem cell
25	chr10:6130400-6132200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr10:6130400-6132200	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr10:6130400-6132200	Active TSS	Aorta	Aorta
28	chr10:6130400-6132200	Active TSS	GM12878-XiMat	blood
29	chr10:6130400-6132400	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr10:6130400-6132400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr10:6130400-6132400	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr10:6130400-6132600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr10:6130400-6132600	Active TSS	Right Atrium	heart
34	chr10:6130400-6132800	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr10:6130600-6131200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr10:6130600-6131200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr10:6130600-6131200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr10:6130600-6131400	Active TSS	HepG2	liver
39	chr10:6130600-6131800	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr10:6130600-6131800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr10:6130600-6131800	Active TSS	Brain Angular Gyrus	brain
42	chr10:6130600-6131800	Active TSS	Brain Cingulate Gyrus	brain
43	chr10:6130600-6131800	Active TSS	Brain Substantia Nigra	brain
44	chr10:6130600-6131800	Active TSS	Colonic Mucosa	Colon
45	chr10:6130600-6131800	Active TSS	Colon Smooth Muscle	Colon
46	chr10:6130600-6131800	Active TSS	Duodenum Mucosa	Duodenum
47	chr10:6130600-6131800	Active TSS	Fetal Brain Female	brain
48	chr10:6130600-6131800	Active TSS	Fetal Stomach	stomach
49	chr10:6130600-6131800	Active TSS	Hela-S3	cervix
50	chr10:6130600-6132000	Active TSS	HUES64 Cell Line	embryonic stem cell

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