Variant report

Variant	rs12264240
Chromosome Location	chr10:6150677-6150678
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr10:6150585-6150938	H1-hESC	embryonic stem cell:	n/a	chr10:6150844-6150851
2	ZNF143	chr10:6150625-6151221	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr10:6150620-6150770	HCM	heart:	n/a	n/a
4	JUND	chr10:6150519-6151201	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr10:6150553-6151459	HCT-116	colon:	n/a	chr10:6151067-6151088 chr10:6151065-6151083 chr10:6150867-6150880 chr10:6151066-6151082 chr10:6151121-6151129
6	CTCF	chr10:6150660-6150810	GM12878	blood:	n/a	n/a
7	CTCF	chr10:6150660-6150810	BJ	skin:	n/a	n/a
8	POLR2A	chr10:6150665-6150917	H1-hESC	embryonic stem cell:	n/a	n/a
9	TEAD4	chr10:6150538-6151054	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr10:6150629-6151374	H1-hESC	embryonic stem cell:	n/a	chr10:6150779-6150788 chr10:6151066-6151085
11	CTCF	chr10:6150620-6150770	HRE	kidney:	n/a	n/a
12	SP1	chr10:6150454-6151300	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr10:6150620-6150770	HFF	foreskin:	n/a	n/a
14	CTCF	chr10:6150620-6150770	HUVEC	blood vessel:	n/a	n/a
15	CTCF	chr10:6150600-6150750	GM12870	blood:	n/a	n/a
16	YY1	chr10:6150549-6150885	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTBP2	chr10:6150611-6151004	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr10:6150620-6150770	NHLF	lung:	n/a	n/a
19	HDAC2	chr10:6150559-6150925	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr10:6150580-6150730	AG04450	lung:	n/a	n/a
21	TCF12	chr10:6150506-6150969	H1-hESC	embryonic stem cell:	n/a	chr10:6150844-6150851
22	CTCF	chr10:6150600-6150750	BJ	skin:	n/a	n/a
23	CTCF	chr10:6150640-6150790	AG04449	skin:	n/a	n/a
24	SP4	chr10:6150483-6151157	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr10:6150144-6152357	K562	blood:	n/a	n/a
26	POLR2A	chr10:6150550-6150964	H1-hESC	embryonic stem cell:	n/a	n/a
27	SP1	chr10:6150498-6151152	H1-hESC	embryonic stem cell:	n/a	n/a
28	SIN3A	chr10:6150599-6151255	H1-hESC	embryonic stem cell:	n/a	n/a
29	TBP	chr10:6150590-6151064	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr10:6150582-6151527	SK-N-SH	brain:	n/a	chr10:6151067-6151088 chr10:6151065-6151083 chr10:6150867-6150880 chr10:6151066-6151082 chr10:6151121-6151129

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:6150676..6151669-chr10:6167991..6168860,2	MCF-7	breast:
2	chr10:6149158..6152677-chr10:6155129..6159616,7	K562	blood:
3	chr10:6145387..6148219-chr10:6148425..6153843,7	K562	blood:
4	chr10:6149017..6157788-chr10:6241652..6246346,17	MCF-7	breast:
5	chr10:6149112..6154904-chr10:6241492..6247373,13	MCF-7	breast:
6	chr10:6150598..6153044-chr10:6184117..6186836,2	K562	blood:
7	chr10:6150619..6154043-chr10:6154851..6158352,3	K562	blood:
8	chr10:6129764..6131854-chr10:6149478..6152087,2	MCF-7	breast:
9	chr10:6149255..6151858-chr10:6188263..6190070,3	K562	blood:
10	chr10:6150553..6151547-chr10:6443502..6444434,6	MCF-7	breast:
11	chr10:6150561..6151530-chr10:6447877..6448813,5	MCF-7	breast:
12	chr10:6149046..6151542-chr10:6153336..6155552,2	MCF-7	breast:
13	chr10:6150489..6151565-chr10:6193116..6194019,6	K562	blood:
14	chr10:6150582..6152965-chr10:6191776..6194691,3	MCF-7	breast:
15	chr10:6149065..6151002-chr10:6243111..6244731,2	K562	blood:
16	chr10:6150645..6151549-chr10:6193064..6193796,3	MCF-7	breast:

No data

Variant related genes	Relation type
RBM17	TF binding region
ENSG00000170525	Chromatin interaction
ENSG00000134453	Chromatin interaction
ENSG00000263628	Chromatin interaction
ENSG00000213994	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10905861	1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11256626	0.88[ASN][1000 genomes]
rs11256664	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256761	1.00[ASN][1000 genomes]
rs11256763	0.92[ASN][1000 genomes]
rs11256801	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11256810	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256854	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11256893	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11256895	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12252274	1.00[ASN][1000 genomes]
rs12254328	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs12262454	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12263912	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12412910	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12416306	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12416514	0.80[AMR][1000 genomes]
rs13376791	0.80[AMR][1000 genomes]
rs3750669	0.89[ASN][1000 genomes]
rs58138632	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59330649	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60859211	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6132800-6152000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:6137400-6158600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:6138000-6159400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr10:6138200-6150800	Strong transcription	Dnd41	blood
5	chr10:6138200-6159200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr10:6138400-6151000	Weak transcription	Fetal Heart	heart
7	chr10:6138400-6152200	Weak transcription	Fetal Brain Male	brain
8	chr10:6138400-6154000	Weak transcription	Small Intestine	intestine
9	chr10:6138800-6152800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr10:6138800-6159200	Strong transcription	Placenta	Placenta
11	chr10:6138800-6159400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr10:6139000-6151400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr10:6139000-6154000	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr10:6139000-6156600	Strong transcription	Fetal Muscle Leg	muscle
15	chr10:6139000-6158600	Strong transcription	Fetal Intestine Large	intestine
16	chr10:6139000-6159200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr10:6139000-6159200	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr10:6139000-6159200	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr10:6139200-6156200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr10:6139200-6156200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr10:6139200-6156200	Strong transcription	Osteobl	bone
22	chr10:6139200-6156400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr10:6139600-6155400	Strong transcription	HSMM	muscle
24	chr10:6139600-6156400	Strong transcription	NH-A	brain
25	chr10:6139800-6156200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr10:6140000-6151400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr10:6140000-6152000	Weak transcription	Aorta	Aorta
28	chr10:6140000-6155800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr10:6140000-6162000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr10:6140400-6161000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr10:6142000-6156400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr10:6142200-6158800	Strong transcription	Stomach Smooth Muscle	stomach
33	chr10:6142200-6159400	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr10:6142400-6151400	Weak transcription	Colonic Mucosa	Colon
35	chr10:6143200-6159400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr10:6143800-6150800	Strong transcription	GM12878-XiMat	blood
37	chr10:6144800-6156400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr10:6145400-6158600	Strong transcription	K562	blood
39	chr10:6145600-6156000	Strong transcription	NHDF-Ad	bronchial
40	chr10:6145600-6156000	Strong transcription	NHLF	lung
41	chr10:6145600-6156400	Strong transcription	Fetal Lung	lung
42	chr10:6145800-6150800	Strong transcription	Liver	Liver
43	chr10:6146000-6151400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr10:6146000-6154400	Strong transcription	HepG2	liver
45	chr10:6146000-6156200	Strong transcription	HUVEC	blood vessel
46	chr10:6146200-6151000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr10:6146200-6154000	Weak transcription	Psoas Muscle	Psoas
48	chr10:6146400-6156400	Strong transcription	Adipose Nuclei	Adipose
49	chr10:6146800-6156800	Strong transcription	Ovary	ovary
50	chr10:6147800-6154200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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