Variant report

Variant	rs11257767
Chromosome Location	chr10:6316910-6316911
allele	A/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	EBF1	chr10:6316721-6317720	GM12878	blood:	n/a	chr10:6317066-6317077
2	SP1	chr10:6316881-6317656	HCT-116	colon:	n/a	chr10:6317156-6317165 chr10:6317155-6317167 chr10:6317156-6317166 chr10:6317155-6317167 chr10:6317157-6317166 chr10:6317156-6317165 chr10:6317156-6317166
3	BCL3	chr10:6316772-6317683	A549	lung:	n/a	n/a
4	ATF2	chr10:6316828-6317760	GM12878	blood:	n/a	n/a
5	POLR2A	chr10:6316379-6317632	GM12878	blood:	n/a	n/a
6	MTA3	chr10:6316850-6317675	GM12878	blood:	n/a	n/a
7	EP300	chr10:6316835-6317683	GM12878	blood:	n/a	n/a
8	JUND	chr10:6316890-6317783	HCT-116	colon:	n/a	chr10:6317450-6317458 chr10:6317445-6317457 chr10:6317445-6317456 chr10:6317446-6317456 chr10:6317446-6317455 chr10:6317447-6317456
9	ELF1	chr10:6316863-6317609	A549	lung:	n/a	chr10:6317373-6317386 chr10:6317349-6317362
10	CTCF	chr10:6316900-6317050	HBMEC	blood vessel:	n/a	chr10:6317018-6317027
11	CTCF	chr10:6316800-6316950	HEEpiC	esophagus:	n/a	n/a
12	ATF2	chr10:6316717-6317747	GM12878	blood:	n/a	n/a
13	STAT3	chr10:6316821-6316942	MCF10A-Er-Src	breast:	n/a	n/a
14	BCLAF1	chr10:6316728-6317670	GM12878	blood:	n/a	n/a
15	STAT3	chr10:6316898-6317785	MCF10A-Er-Src	breast:	n/a	chr10:6317558-6317569
16	MAX	chr10:6316810-6317769	HCT-116	colon:	n/a	chr10:6317169-6317178
17	BATF	chr10:6316799-6317671	GM12878	blood:	n/a	n/a
18	EP300	chr10:6316824-6318461	A549	lung:	n/a	chr10:6318264-6318271
19	POLR2A	chr10:6316601-6317677	GM12878	blood:	n/a	n/a
20	FOXM1	chr10:6316876-6317690	GM12878	blood:	n/a	n/a
21	JUN	chr10:6316659-6317683	K562	blood:	n/a	chr10:6317450-6317458 chr10:6317445-6317457 chr10:6317446-6317456 chr10:6317446-6317455 chr10:6317447-6317456
22	E2F6	chr10:6316810-6318196	A549	lung:	n/a	n/a
23	CTCF	chr10:6316860-6317090	HA-sp	spinal cord:	n/a	chr10:6317018-6317027
24	MAZ	chr10:6316903-6317582	GM12878	blood:	n/a	chr10:6317169-6317178
25	FOXM1	chr10:6316904-6317645	GM12878	blood:	n/a	n/a
26	MAX	chr10:6316798-6318245	A549	lung:	n/a	chr10:6317169-6317178
27	STAT3	chr10:6316809-6317696	GM12878	blood:	n/a	chr10:6317558-6317569
28	EBF1	chr10:6316791-6317672	GM12878	blood:	n/a	chr10:6317066-6317077
29	POU2F2	chr10:6316801-6317652	GM12878	blood:	n/a	n/a
30	EP300	chr10:6316870-6317795	A549	lung:	n/a	n/a
31	SP1	chr10:6316749-6318413	A549	lung:	n/a	chr10:6317156-6317165 chr10:6317155-6317167 chr10:6317156-6317166 chr10:6317155-6317167 chr10:6317157-6317166 chr10:6317156-6317165 chr10:6317156-6317166
32	MTA3	chr10:6316870-6317733	GM12878	blood:	n/a	n/a
33	CEBPB	chr10:6316868-6317704	GM12878	blood:	n/a	chr10:6317549-6317560 chr10:6317038-6317050
34	POLR2A	chr10:6316345-6317717	GM12878	blood:	n/a	n/a
35	POLR2A	chr10:6316821-6317745	U87	brain:	n/a	n/a
36	CTCF	chr10:6316880-6317030	AG04450	lung:	n/a	chr10:6317018-6317027
37	CTCF	chr10:6316900-6317050	A549	lung:	n/a	chr10:6317018-6317027
38	STAT5A	chr10:6316803-6317622	GM12878	blood:	n/a	chr10:6317558-6317569
39	POLR2A	chr10:6316857-6317812	U87	brain:	n/a	n/a
40	TCF12	chr10:6316909-6317797	SK-N-SH	brain:	n/a	chr10:6317140-6317150
41	BCL3	chr10:6316886-6317649	GM12878	blood:	n/a	n/a
42	SP1	chr10:6316782-6317833	A549	lung:	n/a	chr10:6317156-6317165 chr10:6317155-6317167 chr10:6317156-6317166 chr10:6317155-6317167 chr10:6317157-6317166 chr10:6317156-6317165 chr10:6317156-6317166
43	ZNF384	chr10:6316727-6317772	GM12878	blood:	n/a	n/a
44	SRF	chr10:6316797-6317766	HCT-116	colon:	n/a	chr10:6317157-6317167
45	TBP	chr10:6316854-6317584	GM12878	blood:	n/a	n/a
46	CTCF	chr10:6316900-6317050	HMF	breast:	n/a	chr10:6317018-6317027
47	GABPA	chr10:6316856-6317758	A549	lung:	n/a	n/a
48	CTCF	chr10:6316880-6317030	AG10803	skin:	n/a	chr10:6317018-6317027
49	USF2	chr10:6316845-6317576	GM12878	blood:	n/a	n/a
50	FOS	chr10:6316901-6317782	HUVEC	blood vessel:	n/a	chr10:6317445-6317456 chr10:6317450-6317458 chr10:6317445-6317457 chr10:6317446-6317456 chr10:6317446-6317455 chr10:6317447-6317456

No.	Distal block	Cell Line	Cell type
1	chr10:6242922..6247696-chr10:6316001..6319432,5	MCF-7	breast:
2	chr10:6298094..6299703-chr10:6315847..6318210,2	K562	blood:
3	chr10:6316397..6317934-chr10:6328734..6330716,2	MCF-7	breast:
4	chr10:6282149..6284727-chr10:6315762..6318324,2	MCF-7	breast:
5	chr10:6263461..6265424-chr10:6315540..6318347,2	K562	blood:
6	chr10:6315744..6318557-chr10:6324362..6327145,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215244	TF binding region
ENSG00000213994	Chromatin interaction
ENSG00000170525	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11257712	0.85[EUR][1000 genomes]
rs11257726	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11257734	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11257741	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11257742	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1040721	chr10:6155144-6322566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
3	nsv540476	chr10:6155144-6322566	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh 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	40 gene(s)	inside rSNPs	diseases
5	nsv1041039	chr10:6217724-6354858	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv894836	chr10:6246678-6435374	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv430123	chr10:6309402-6448384	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6309600-6317000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr10:6309600-6317000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:6309600-6317200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr10:6312800-6317000	Weak transcription	Spleen	Spleen
5	chr10:6313400-6317000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr10:6313400-6317200	Weak transcription	Fetal Intestine Small	intestine
7	chr10:6313400-6317200	Weak transcription	Thymus	Thymus
8	chr10:6313600-6317000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr10:6313600-6317000	Weak transcription	Fetal Thymus	thymus
10	chr10:6313800-6317000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:6313800-6317000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr10:6313800-6317000	Weak transcription	Primary T cells from cord blood	blood
13	chr10:6313800-6317000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr10:6313800-6317000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr10:6313800-6321000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr10:6314200-6317000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr10:6314200-6317000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr10:6314200-6317000	Weak transcription	Brain Hippocampus Middle	brain
19	chr10:6314200-6317000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr10:6314200-6317000	Weak transcription	Esophagus	oesophagus
21	chr10:6314200-6317000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr10:6314200-6317000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr10:6314200-6317000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr10:6314400-6317000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr10:6314400-6317000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr10:6314400-6317000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr10:6314400-6321800	Weak transcription	Gastric	stomach
28	chr10:6315200-6317600	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr10:6315200-6318000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr10:6315200-6318800	Enhancers	Fetal Lung	lung
31	chr10:6315400-6317000	Weak transcription	Fetal Stomach	stomach
32	chr10:6315400-6317600	Enhancers	HepG2	liver
33	chr10:6315400-6318200	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr10:6315800-6317000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr10:6315800-6317000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr10:6315800-6317000	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr10:6315800-6317000	Weak transcription	Right Atrium	heart
38	chr10:6315800-6317000	Enhancers	Hela-S3	cervix
39	chr10:6315800-6317200	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr10:6316000-6317600	Weak transcription	Liver	Liver
41	chr10:6316400-6317000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr10:6316400-6318000	Enhancers	Primary B cells from cord blood	blood
43	chr10:6316400-6318200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr10:6316400-6318200	Enhancers	Primary hematopoietic stem cells	blood
45	chr10:6316400-6318600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr10:6316600-6317000	Enhancers	Primary T cells fromperipheralblood	blood
47	chr10:6316600-6317000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr10:6316600-6317000	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr10:6316600-6317200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr10:6316600-6317200	Enhancers	Aorta	Aorta

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