Variant report

Variant	rs61553400
Chromosome Location	chr1:78052058-78052059
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78051276..78052829-chr1:78469916..78471665,2	K562	blood:
2	chr1:78045237..78047732-chr1:78051169..78053649,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162616	Chromatin interaction
ENSG00000273338	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs35178440	1.00[EUR][1000 genomes]
rs55790102	1.00[AFR][1000 genomes]
rs55872024	1.00[EUR][1000 genomes]
rs56010524	1.00[EUR][1000 genomes]
rs58120905	1.00[EUR][1000 genomes]
rs59338720	1.00[EUR][1000 genomes]
rs59883033	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60000721	1.00[EUR][1000 genomes]
rs60658102	1.00[EUR][1000 genomes]
rs61655329	1.00[EUR][1000 genomes]
rs74090643	0.86[AFR][1000 genomes]
rs74090646	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74090649	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74090651	0.86[AFR][1000 genomes]
rs74090653	1.00[EUR][1000 genomes]
rs74090654	1.00[AFR][1000 genomes]
rs74090658	0.86[AFR][1000 genomes]
rs74090661	1.00[AFR][1000 genomes]
rs74090669	1.00[EUR][1000 genomes]
rs74090673	1.00[EUR][1000 genomes]
rs74090678	1.00[EUR][1000 genomes]
rs74090686	1.00[EUR][1000 genomes]
rs74092304	1.00[EUR][1000 genomes]
rs74092305	1.00[EUR][1000 genomes]
rs74092316	1.00[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	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870709	chr1:78016517-78198322	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3337461	chr1:78036000-78153859	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78006200-78064400	Weak transcription	Stomach Mucosa	stomach
2	chr1:78024800-78071000	Weak transcription	Gastric	stomach
3	chr1:78028600-78054600	Weak transcription	Esophagus	oesophagus
4	chr1:78032000-78062800	Weak transcription	Fetal Heart	heart
5	chr1:78032600-78070800	Weak transcription	Aorta	Aorta
6	chr1:78032800-78070600	Weak transcription	Small Intestine	intestine
7	chr1:78033000-78057000	Weak transcription	Spleen	Spleen
8	chr1:78033000-78057200	Weak transcription	Psoas Muscle	Psoas
9	chr1:78033200-78072600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:78033400-78057600	Weak transcription	Right Ventricle	heart
11	chr1:78033400-78069600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:78033600-78070800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:78034000-78056200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:78036400-78052800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr1:78037800-78055400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:78038600-78053000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:78038600-78071000	Weak transcription	Pancreas	Pancrea
18	chr1:78039000-78070800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:78042000-78070800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:78042000-78074600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:78042200-78073800	Weak transcription	Fetal Brain Female	brain
22	chr1:78043000-78070200	Weak transcription	Brain Substantia Nigra	brain
23	chr1:78044200-78054600	Weak transcription	Fetal Intestine Small	intestine
24	chr1:78044200-78055200	Weak transcription	Ovary	ovary
25	chr1:78044200-78069000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:78044400-78063000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:78046400-78056000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:78046800-78054600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:78047000-78056000	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:78047000-78070800	Weak transcription	Lung	lung
31	chr1:78047000-78071200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:78047600-78052600	Weak transcription	Primary T cells from cord blood	blood
33	chr1:78047600-78052800	Weak transcription	NHEK	skin
34	chr1:78047600-78053400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:78047600-78056200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:78047600-78056600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:78047600-78056800	Weak transcription	K562	blood
38	chr1:78047600-78060200	Weak transcription	HUVEC	blood vessel
39	chr1:78047600-78061800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr1:78047600-78062200	Weak transcription	Fetal Muscle Leg	muscle
41	chr1:78047600-78063000	Weak transcription	Fetal Brain Male	brain
42	chr1:78047600-78063200	Weak transcription	Brain Anterior Caudate	brain
43	chr1:78047600-78069000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:78047600-78070800	Weak transcription	HSMMtube	muscle
45	chr1:78047600-78071000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr1:78047600-78071600	Weak transcription	Thymus	Thymus
47	chr1:78047600-78072400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:78047600-78072600	Weak transcription	Fetal Kidney	kidney
49	chr1:78047600-78074600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr1:78047600-78074800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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