Variant report

Variant	rs12416306
Chromosome Location	chr10:6157147-6157148
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr10:6155651..6158898-chr10:6185032..6187374,4	MCF-7	breast:
2	chr10:6149158..6152677-chr10:6155129..6159616,7	K562	blood:
3	chr10:6157094..6159629-chr10:6160136..6162344,2	MCF-7	breast:
4	chr10:6137633..6139244-chr10:6156311..6159157,2	K562	blood:
5	chr10:6157111..6159833-chr10:6166707..6168327,2	MCF-7	breast:
6	chr10:6149017..6157788-chr10:6241652..6246346,17	MCF-7	breast:
7	chr10:6156442..6158166-chr10:6243726..6246113,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PFKFB3-2	chr10:6156110-6157274	NONHSAT011206

No data

Variant related genes	Relation type
ENSG00000134453	Chromatin interaction
ENSG00000213994	Chromatin interaction
ENSG00000170525	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10905861	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11256626	0.88[ASN][1000 genomes]
rs11256664	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256685	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256761	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11256763	0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11256801	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11256810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256854	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11256893	1.00[EUR][1000 genomes]
rs11256895	0.84[ASN][1000 genomes]
rs12252274	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12254328	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12262454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12263912	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264240	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12412910	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3750669	0.89[ASN][1000 genomes]
rs58138632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59330649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60859211	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60960627	0.96[AFR][1000 genomes];0.85[AMR][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	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	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
6	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
7	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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6137400-6158600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:6138000-6159400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr10:6138200-6159200	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr10:6138800-6159200	Strong transcription	Placenta	Placenta
5	chr10:6138800-6159400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr10:6139000-6158600	Strong transcription	Fetal Intestine Large	intestine
7	chr10:6139000-6159200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr10:6139000-6159200	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr10:6139000-6159200	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr10:6140000-6162000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr10:6140400-6161000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr10:6142200-6158800	Strong transcription	Stomach Smooth Muscle	stomach
13	chr10:6142200-6159400	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr10:6143200-6159400	Strong transcription	Fetal Muscle Trunk	muscle
15	chr10:6145400-6158600	Strong transcription	K562	blood
16	chr10:6148000-6157600	Strong transcription	Thymus	Thymus
17	chr10:6148000-6158800	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr10:6148000-6159000	Strong transcription	Brain Germinal Matrix	brain
19	chr10:6148400-6157600	Strong transcription	Fetal Stomach	stomach
20	chr10:6149000-6157600	Strong transcription	Lung	lung
21	chr10:6149800-6157200	Strong transcription	Fetal Brain Female	brain
22	chr10:6149800-6158600	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr10:6150000-6157600	Strong transcription	Colon Smooth Muscle	Colon
24	chr10:6150000-6158400	Strong transcription	Rectal Smooth Muscle	rectum
25	chr10:6150600-6157600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr10:6151000-6158200	Strong transcription	HMEC	breast
27	chr10:6151000-6158600	Strong transcription	NHEK	skin
28	chr10:6151000-6159200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr10:6151000-6159200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr10:6151000-6159400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr10:6151000-6159600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr10:6151200-6157200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
33	chr10:6151200-6157600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
34	chr10:6151200-6158400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr10:6151200-6159200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr10:6151400-6157600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr10:6151400-6158200	Strong transcription	Colonic Mucosa	Colon
38	chr10:6151400-6158400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr10:6151400-6159000	Strong transcription	Primary B cells from peripheral blood	blood
40	chr10:6151400-6159000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr10:6151400-6159200	Strong transcription	Primary B cells from cord blood	blood
42	chr10:6151400-6159200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr10:6151400-6159200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr10:6151400-6159400	Strong transcription	Dnd41	blood
45	chr10:6151400-6160000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr10:6151600-6158600	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr10:6151600-6158800	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr10:6151600-6159200	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr10:6151600-6159200	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr10:6151600-6159200	Strong transcription	Primary hematopoietic stem cells	blood

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