Variant report

Variant	rs744405
Chromosome Location	chr6:5265956-5265957
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5259731..5262247-chr6:5263109..5267225,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145982	Chromatin interaction
ENSG00000214113	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1411337	0.97[ASN][1000 genomes]
rs17139778	0.91[ASN][1000 genomes]
rs17139809	0.92[ASN][1000 genomes]
rs17139811	0.92[ASN][1000 genomes]
rs17312134	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1884977	0.88[ASN][1000 genomes]
rs1983982	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2145373	0.95[ASN][1000 genomes]
rs2208362	0.92[ASN][1000 genomes]
rs2746225	0.90[ASN][1000 genomes]
rs2746227	0.90[ASN][1000 genomes]
rs2746228	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2753241	0.92[ASN][1000 genomes]
rs2753242	0.92[ASN][1000 genomes]
rs2773288	0.90[ASN][1000 genomes]
rs2773292	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2773297	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2773315	0.92[ASN][1000 genomes]
rs384574	0.88[ASN][1000 genomes]
rs409993	0.87[ASN][1000 genomes]
rs4141760	0.96[ASN][1000 genomes]
rs444607	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs446312	0.88[ASN][1000 genomes]
rs4499975	0.96[ASN][1000 genomes]
rs4502984	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4530910	0.97[ASN][1000 genomes]
rs4585611	0.86[ASN][1000 genomes]
rs4607474	0.92[ASN][1000 genomes]
rs4610609	0.90[ASN][1000 genomes]
rs72813608	0.92[ASN][1000 genomes]
rs730594	1.00[ASN][1000 genomes]
rs730595	1.00[ASN][1000 genomes]
rs744756	0.96[ASN][1000 genomes]
rs744757	0.96[ASN][1000 genomes]
rs744758	0.85[ASN][1000 genomes]
rs7775335	0.96[ASN][1000 genomes]
rs9328292	0.93[ASN][1000 genomes]
rs9405815	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9405817	0.97[ASN][1000 genomes]
rs9502285	0.90[ASN][1000 genomes]
rs9504357	0.90[ASN][1000 genomes]
rs9504374	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1021646	chr6:5157795-5367254	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv538115	chr6:5157795-5367254	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1029609	chr6:5187633-5397254	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1035080	chr6:5206533-5396019	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv538116	chr6:5206533-5396019	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv1016456	chr6:5216835-5315913	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv538117	chr6:5216835-5315913	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv1028185	chr6:5247624-5340163	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv830578	chr6:5264086-5455570	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5262400-5268200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:5262400-5287200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:5262400-5302400	Weak transcription	Aorta	Aorta
4	chr6:5262600-5266400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:5262600-5268200	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:5262600-5271200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:5262600-5275200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:5262600-5287200	Weak transcription	Esophagus	oesophagus
9	chr6:5262600-5287600	Weak transcription	Ovary	ovary
10	chr6:5262800-5266800	Weak transcription	Thymus	Thymus
11	chr6:5262800-5268800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:5262800-5273600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr6:5262800-5274400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:5262800-5277000	Weak transcription	Pancreas	Pancrea
15	chr6:5262800-5279000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:5262800-5287200	Weak transcription	Spleen	Spleen
17	chr6:5262800-5287400	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:5263000-5272000	Weak transcription	HMEC	breast
19	chr6:5263000-5273400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr6:5263000-5274400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:5263000-5277200	Weak transcription	Adipose Nuclei	Adipose
22	chr6:5263000-5279000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:5263000-5285200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr6:5263000-5287200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr6:5263000-5287400	Weak transcription	Fetal Stomach	stomach
26	chr6:5263000-5287800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr6:5263000-5301000	Weak transcription	Fetal Brain Male	brain
28	chr6:5263200-5266000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:5263200-5266400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:5263200-5266400	Weak transcription	Liver	Liver
31	chr6:5263200-5266600	Weak transcription	Fetal Intestine Large	intestine
32	chr6:5263200-5270400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:5263200-5271600	Weak transcription	NHEK	skin
34	chr6:5263200-5271800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:5263200-5273800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:5263200-5274400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:5263200-5278400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr6:5263200-5278400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr6:5263200-5279000	Weak transcription	Brain Anterior Caudate	brain
40	chr6:5263200-5280200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:5263200-5287800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr6:5263400-5266000	Weak transcription	Primary T cells from cord blood	blood
43	chr6:5263400-5266400	Weak transcription	HepG2	liver
44	chr6:5263400-5269800	Weak transcription	K562	blood
45	chr6:5263400-5270200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:5263400-5271000	Weak transcription	Primary B cells from cord blood	blood
47	chr6:5263400-5276800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:5263400-5281200	Weak transcription	Brain Angular Gyrus	brain
49	chr6:5263400-5287400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:5263400-5287600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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