Variant report

Variant	rs12779865
Chromosome Location	chr10:21829162-21829163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:21822263..21825196-chr10:21825343..21829411,7	MCF-7	breast:
2	chr10:21828206..21830933-chr10:21844979..21847249,2	MCF-7	breast:
3	chr10:21815110..21817816-chr10:21828150..21829882,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000078403	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10828247	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10828248	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10828249	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10828250	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10828252	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10828256	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11012726	0.83[ASN][1000 genomes]
rs11012732	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11012737	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11012750	0.92[AFR][1000 genomes]
rs11592565	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12251016	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12253527	0.81[EUR][1000 genomes]
rs12356674	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12357321	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1243179	0.92[AFR][1000 genomes]
rs1243185	0.85[AFR][1000 genomes]
rs1243187	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1243189	0.88[AFR][1000 genomes]
rs1269454	0.92[AFR][1000 genomes]
rs12769128	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12783517	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12784277	1.00[ASN][1000 genomes]
rs1416901	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1802669	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34719019	0.83[AFR][1000 genomes]
rs34853448	0.81[AMR][1000 genomes]
rs35587371	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61850044	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482188	0.83[ASN][1000 genomes]
rs7084454	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7098100	0.90[EUR][1000 genomes]
rs7905967	0.81[EUR][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	nsv825284	chr10:21739527-21847437	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv825285	chr10:21742026-21874334	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv825286	chr10:21757784-21838890	Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
4	nsv825288	chr10:21759085-21831354	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
5	nsv825289	chr10:21762506-21845875	Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
6	nsv825290	chr10:21777857-21830878	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
7	nsv894939	chr10:21789406-21830104	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv825291	chr10:21792100-21830946	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv894945	chr10:21798241-21830104	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv894946	chr10:21798241-21831215	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	nsv1052477	chr10:21810270-21889726	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12779865	MLLT10	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:21822800-21837800	Weak transcription	Stomach Mucosa	stomach
2	chr10:21824600-21829800	Weak transcription	Colonic Mucosa	Colon
3	chr10:21824600-21842600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr10:21824600-21864600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr10:21824600-21930400	Weak transcription	Gastric	stomach
6	chr10:21824800-21829200	Weak transcription	HSMMtube	muscle
7	chr10:21824800-21830000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:21824800-21830400	Weak transcription	Fetal Kidney	kidney
9	chr10:21824800-21830600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr10:21824800-21831600	Weak transcription	Aorta	Aorta
11	chr10:21824800-21839200	Weak transcription	Hela-S3	cervix
12	chr10:21824800-21841800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr10:21824800-21852200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:21824800-21852200	Strong transcription	Fetal Intestine Small	intestine
15	chr10:21824800-21860200	Weak transcription	Psoas Muscle	Psoas
16	chr10:21825000-21829200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr10:21825000-21829200	Weak transcription	NHEK	skin
18	chr10:21825000-21838800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr10:21825000-21844200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr10:21825000-21850000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr10:21825200-21829200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr10:21825200-21829200	Weak transcription	Brain Substantia Nigra	brain
23	chr10:21825200-21829200	Weak transcription	Fetal Brain Female	brain
24	chr10:21825200-21835800	Strong transcription	Placenta	Placenta
25	chr10:21825200-21850600	Strong transcription	Fetal Stomach	stomach
26	chr10:21825200-21854800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr10:21825400-21836000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr10:21825400-21836200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr10:21825400-21836800	Strong transcription	Fetal Muscle Leg	muscle
30	chr10:21825400-21837000	Strong transcription	Fetal Thymus	thymus
31	chr10:21825400-21839000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr10:21825400-21839200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr10:21825600-21830800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr10:21825600-21831000	Weak transcription	Fetal Heart	heart
35	chr10:21825600-21831800	Weak transcription	NHLF	lung
36	chr10:21825600-21835400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr10:21825600-21836200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr10:21825600-21836400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr10:21825600-21836400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr10:21825600-21842200	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr10:21825600-21849800	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr10:21825600-21850000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr10:21825600-21857800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr10:21825800-21830200	Weak transcription	Esophagus	oesophagus
45	chr10:21825800-21830800	Weak transcription	K562	blood
46	chr10:21825800-21831600	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr10:21825800-21835000	Strong transcription	Stomach Smooth Muscle	stomach
48	chr10:21825800-21835200	Strong transcription	Dnd41	blood
49	chr10:21825800-21844400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr10:21825800-21856200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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