Variant report

Variant	rs62397952
Chromosome Location	chr6:20205378-20205379
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:20203563..20206976-chr6:20208756..20213535,5	MCF-7	breast:
2	chr6:20204116..20205859-chr6:20336022..20338444,2	K562	blood:
3	chr6:20201447..20207053-chr6:20401187..20404960,5	K562	blood:
4	chr6:20198875..20206310-chr6:20399680..20405305,15	K562	blood:

Variant related genes	Relation type
ENSG00000112242	Chromatin interaction
ENSG00000227803	Chromatin interaction
ENSG00000172197	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs55684688	0.80[EUR][1000 genomes]
rs62397943	0.82[EUR][1000 genomes]
rs62397945	0.94[EUR][1000 genomes]
rs62397946	0.94[EUR][1000 genomes]
rs62397948	0.91[EUR][1000 genomes]
rs62397949	0.88[EUR][1000 genomes]
rs62397950	0.91[EUR][1000 genomes]
rs62397951	0.91[EUR][1000 genomes]
rs72826629	0.94[EUR][1000 genomes]
rs72826635	0.91[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	nsv1029729	chr6:20113226-20235122	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv538155	chr6:20113226-20235122	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1033904	chr6:20127596-20210374	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1799840	chr6:20196549-20210374	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:20193000-20209200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:20198600-20206400	Enhancers	Colon Smooth Muscle	Colon
3	chr6:20199400-20206000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:20199400-20207600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:20199400-20210000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:20199600-20207600	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr6:20200600-20206200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:20200600-20209200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr6:20201000-20206000	Enhancers	Duodenum Mucosa	Duodenum
10	chr6:20201200-20205400	Enhancers	Fetal Intestine Large	intestine
11	chr6:20201200-20205800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:20201200-20205800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:20201200-20206000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr6:20201200-20206000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:20201200-20206800	Enhancers	Primary hematopoietic stem cells	blood
16	chr6:20201200-20207000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:20201400-20210800	Weak transcription	Fetal Stomach	stomach
18	chr6:20201600-20206800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr6:20201600-20207800	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr6:20201800-20205800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:20201800-20209000	Weak transcription	Fetal Lung	lung
22	chr6:20202000-20205400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:20202000-20206800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:20202200-20206000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:20202400-20205800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:20202400-20206800	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr6:20202600-20206000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr6:20202600-20206600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:20202600-20207000	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr6:20202600-20211200	Enhancers	Stomach Mucosa	stomach
31	chr6:20203000-20205600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:20203200-20206600	Enhancers	Primary T cells fromperipheralblood	blood
33	chr6:20203200-20210400	Weak transcription	Fetal Kidney	kidney
34	chr6:20203200-20211200	Weak transcription	Liver	Liver
35	chr6:20203200-20211200	Weak transcription	NHDF-Ad	bronchial
36	chr6:20203600-20205600	Enhancers	GM12878-XiMat	blood
37	chr6:20203600-20208000	Enhancers	Rectal Smooth Muscle	rectum
38	chr6:20203600-20210400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:20203800-20205800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr6:20203800-20206600	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr6:20203800-20208200	Enhancers	Ovary	ovary
42	chr6:20204000-20206400	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr6:20204000-20207800	Enhancers	Fetal Thymus	thymus
44	chr6:20204000-20208200	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr6:20204200-20206200	Enhancers	Colonic Mucosa	Colon
46	chr6:20204200-20206400	Enhancers	Right Ventricle	heart
47	chr6:20204200-20207000	Enhancers	Adipose Nuclei	Adipose
48	chr6:20204200-20207200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:20204200-20207800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:20204400-20205400	Enhancers	Left Ventricle	heart

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