Variant report

Variant	rs57185346
Chromosome Location	chr10:52180300-52180301
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr10:52179539-52180355	K562	blood:	n/a	n/a
2	BHLHE40	chr10:52180031-52180345	K562	blood:	n/a	n/a
3	USF1	chr10:52180019-52180432	K562	blood:	n/a	n/a
4	JUND	chr10:52179527-52180312	K562	blood:	n/a	chr10:52180126-52180136 chr10:52180127-52180135
5	CTCF	chr10:52180180-52180330	K562	blood:	n/a	n/a
6	MAZ	chr10:52179977-52180490	K562	blood:	n/a	chr10:52180175-52180185 chr10:52180213-52180222

No.	Distal block	Cell Line	Cell type
1	chr10:52049655..52052352-chr10:52178412..52180723,2	MCF-7	breast:
2	chr10:52175389..52176966-chr10:52179598..52182050,2	K562	blood:
3	chr10:52179920..52182656-chr10:52203017..52204731,2	K562	blood:
4	chr10:52179209..52181843-chr10:52226952..52229570,2	MCF-7	breast:
5	chr10:52176749..52178866-chr10:52179847..52182390,3	MCF-7	breast:

Variant related genes	Relation type
SGMS1	TF binding region
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs56040538	0.80[AFR][1000 genomes]
rs56257817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57222480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58417005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59310089	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59583053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74131292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74131295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74132709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74132710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74132713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74132715	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52178400-52180400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr10:52178400-52181000	Weak transcription	Esophagus	oesophagus
3	chr10:52178400-52220000	Weak transcription	Pancreas	Pancrea
4	chr10:52178600-52180600	Weak transcription	Primary B cells from cord blood	blood
5	chr10:52178600-52180600	Weak transcription	Brain Anterior Caudate	brain
6	chr10:52178600-52180600	Enhancers	Fetal Intestine Large	intestine
7	chr10:52178600-52180600	Weak transcription	Fetal Kidney	kidney
8	chr10:52178600-52181000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr10:52178600-52181000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr10:52178600-52181000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr10:52178600-52181000	Weak transcription	Brain Angular Gyrus	brain
12	chr10:52178600-52181000	Weak transcription	Psoas Muscle	Psoas
13	chr10:52178600-52181000	Weak transcription	Stomach Mucosa	stomach
14	chr10:52178600-52181000	Weak transcription	Spleen	Spleen
15	chr10:52178600-52181200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr10:52178600-52181400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr10:52178600-52181400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr10:52178600-52181400	Weak transcription	Gastric	stomach
19	chr10:52178600-52181400	Weak transcription	Lung	lung
20	chr10:52178600-52181600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr10:52178600-52181600	Weak transcription	Fetal Stomach	stomach
22	chr10:52178600-52181800	Weak transcription	Fetal Brain Female	brain
23	chr10:52178600-52182000	Enhancers	Brain Hippocampus Middle	brain
24	chr10:52178600-52182400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr10:52178600-52182600	Enhancers	Fetal Lung	lung
26	chr10:52178600-52183400	Enhancers	Brain Cingulate Gyrus	brain
27	chr10:52178600-52188800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr10:52178600-52217200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr10:52178600-52219400	Weak transcription	Left Ventricle	heart
30	chr10:52178800-52180600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr10:52178800-52181000	Weak transcription	Small Intestine	intestine
32	chr10:52178800-52181000	Weak transcription	NHDF-Ad	bronchial
33	chr10:52178800-52181200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr10:52178800-52181600	Enhancers	Brain Substantia Nigra	brain
35	chr10:52178800-52181600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr10:52178800-52182000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr10:52178800-52182400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr10:52178800-52183800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr10:52178800-52187400	Weak transcription	Primary T cells from cord blood	blood
40	chr10:52178800-52191200	Weak transcription	HSMMtube	muscle
41	chr10:52178800-52198000	Weak transcription	Fetal Thymus	thymus
42	chr10:52178800-52202800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr10:52179000-52180600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr10:52179000-52180600	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr10:52179000-52181000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr10:52179000-52181600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr10:52179000-52191000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr10:52179000-52191200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr10:52179000-52191400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr10:52179000-52191600	Weak transcription	Duodenum Mucosa	Duodenum

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