Variant report

Variant	rs11257259
Chromosome Location	chr10:6247518-6247519
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr10:6244277-6247528	A549	lung:	n/a	n/a
2	CHD1	chr10:6244151-6247539	IMR90	lung:	n/a	n/a
3	POLR2A	chr10:6244539-6247821	IMR90	lung:	n/a	n/a
4	SIN3AK20	chr10:6246136-6247545	A549	lung:	n/a	n/a
5	POLR2A	chr10:6244620-6247622	GM12878	blood:	n/a	n/a
6	POLR2A	chr10:6244173-6247852	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:6245082..6247661-chr9:91147129..91149982,2	MCF-7	breast:
2	chr10:6245084..6247522-chr10:6358973..6361369,2	MCF-7	breast:
3	chr10:6242187..6248014-chr10:6262246..6271624,18	MCF-7	breast:
4	chr10:6132741..6135647-chr10:6244936..6248119,3	MCF-7	breast:
5	chr10:6245444..6247830-chr10:6297779..6300544,2	MCF-7	breast:
6	chr10:6245319..6247600-chr17:59477846..59479369,2	MCF-7	breast:
7	chr10:6242739..6248482-chr10:6257769..6263853,7	MCF-7	breast:

No data

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

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2794983	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4747921	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4750075	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57770060	0.90[ASN][1000 genomes]
rs61297532	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72777862	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv894817	chr10:6173416-6251252	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
6	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
7	nsv894832	chr10:6237156-6253651	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv894833	chr10:6237156-6261704	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv894834	chr10:6237156-6272169	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv894835	chr10:6242176-6268422	Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	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

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6242800-6247800	Active TSS	Aorta	Aorta
2	chr10:6244600-6247600	Active TSS	Esophagus	oesophagus
3	chr10:6244600-6249400	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr10:6246000-6272200	Weak transcription	K562	blood
5	chr10:6246400-6247600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr10:6246400-6247600	Enhancers	Spleen	Spleen
7	chr10:6246400-6247800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr10:6246600-6247600	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr10:6246600-6253200	Weak transcription	Primary T cells from cord blood	blood
10	chr10:6246600-6253400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr10:6246800-6253600	Weak transcription	Colonic Mucosa	Colon
12	chr10:6246800-6256800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr10:6247000-6247600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr10:6247000-6247600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr10:6247000-6247800	Active TSS	Brain Hippocampus Middle	brain
16	chr10:6247000-6249400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr10:6247000-6249600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr10:6247000-6250600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr10:6247000-6252200	Weak transcription	Fetal Stomach	stomach
20	chr10:6247000-6253000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr10:6247000-6253200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr10:6247000-6253200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr10:6247000-6253200	Weak transcription	Gastric	stomach
24	chr10:6247000-6253200	Weak transcription	Right Atrium	heart
25	chr10:6247000-6253200	Weak transcription	Right Ventricle	heart
26	chr10:6247000-6253400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr10:6247000-6253400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr10:6247000-6254800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr10:6247000-6255600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr10:6247000-6255600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr10:6247000-6255600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr10:6247000-6255600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr10:6247000-6255800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr10:6247000-6258000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr10:6247000-6280600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:6247200-6247600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr10:6247200-6247600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr10:6247200-6247600	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr10:6247200-6247600	Enhancers	Duodenum Mucosa	Duodenum
40	chr10:6247200-6247600	Weak transcription	Lung	lung
41	chr10:6247200-6247600	Enhancers	Psoas Muscle	Psoas
42	chr10:6247200-6247600	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr10:6247200-6247600	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr10:6247200-6247800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr10:6247200-6247800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr10:6247200-6247800	Active TSS	Adipose Nuclei	Adipose
47	chr10:6247200-6248000	Active TSS	Primary B cells from cord blood	blood
48	chr10:6247200-6248000	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr10:6247200-6248000	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr10:6247200-6248600	Weak transcription	Stomach Smooth Muscle	stomach

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