Variant report

Variant	rs12110774
Chromosome Location	chr6:24874155-24874156
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24872106..24874962-chr6:24876446..24878198,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111913	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10946732	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10946735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12110779	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12111413	0.86[EUR][1000 genomes]
rs13220782	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16889761	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17671350	0.80[EUR][1000 genomes]
rs28385634	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35158242	0.84[EUR][1000 genomes]
rs35250553	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35953835	0.80[EUR][1000 genomes]
rs6456637	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6918387	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6918511	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71555168	0.80[EUR][1000 genomes]
rs7760221	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][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	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24843800-24879400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:24847000-24876600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:24855200-24895000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
4	chr6:24855800-24874200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:24856200-24876400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:24856200-24882400	Weak transcription	NHLF	lung
7	chr6:24856400-24877200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:24858600-24876000	Weak transcription	Right Ventricle	heart
9	chr6:24858800-24876600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:24859200-24877000	Weak transcription	Gastric	stomach
11	chr6:24859200-24877000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:24859200-24877200	Weak transcription	Lung	lung
13	chr6:24859400-24874800	Weak transcription	Adipose Nuclei	Adipose
14	chr6:24859400-24886800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:24860400-24876600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:24861200-24877000	Weak transcription	Psoas Muscle	Psoas
17	chr6:24861400-24876800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr6:24861600-24875400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:24861600-24877000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr6:24862800-24876000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr6:24862800-24877000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:24862800-24885600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr6:24862800-24887400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
24	chr6:24863000-24876600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:24863800-24875800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:24863800-24876400	Strong transcription	Fetal Thymus	thymus
27	chr6:24864000-24877200	Weak transcription	Fetal Stomach	stomach
28	chr6:24864400-24877000	Strong transcription	Primary hematopoietic stem cells	blood
29	chr6:24865600-24876000	Weak transcription	Left Ventricle	heart
30	chr6:24865600-24877000	Strong transcription	Primary B cells from cord blood	blood
31	chr6:24865600-24879600	Weak transcription	Brain Germinal Matrix	brain
32	chr6:24865800-24877000	Weak transcription	Liver	Liver
33	chr6:24867600-24876200	Strong transcription	GM12878-XiMat	blood
34	chr6:24868800-24874600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:24869000-24878000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:24869400-24875400	Strong transcription	Primary B cells from peripheral blood	blood
37	chr6:24869400-24876800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr6:24870000-24875400	Strong transcription	NHDF-Ad	bronchial
39	chr6:24870200-24874400	Genic enhancers	Primary T cells from cord blood	blood
40	chr6:24870400-24875200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:24870400-24878200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr6:24870400-24883800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr6:24870800-24874800	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:24870800-24876200	Strong transcription	HSMMtube	muscle
45	chr6:24870800-24876600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:24870800-24877000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr6:24870800-24877200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:24871400-24876600	Strong transcription	Thymus	Thymus
49	chr6:24871800-24876000	Strong transcription	Spleen	Spleen
50	chr6:24871800-24886800	Weak transcription	Brain Cingulate Gyrus	brain

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