Variant report

Variant	rs2140406
Chromosome Location	chr10:52105560-52105561
allele	A/G
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	RFX5	chr10:52105459-52105727	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:52105040..52107754-chr10:52130504..52132718,2	MCF-7	breast:
2	chr10:52100945..52103388-chr10:52103997..52106988,2	MCF-7	breast:
3	chr10:52104092..52107025-chr10:52382873..52384665,2	MCF-7	breast:

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

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10740654	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10763354	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1436211	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2177371	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4935623	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55775518	0.89[AFR][1000 genomes]
rs7082941	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518071	chr10:51595893-52157935	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	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
3	nsv1053903	chr10:51886486-52163991	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1040661	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1051028	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1037118	chr10:51886486-52167442	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	esv2830205	chr10:51978430-52135215	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv1046850	chr10:52009869-52135542	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv540625	chr10:52009869-52135542	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
14	esv2762864	chr10:52030945-52107415	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
15	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:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52087000-52105800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr10:52087000-52106800	Weak transcription	Brain Angular Gyrus	brain
3	chr10:52087200-52107400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr10:52087600-52106600	Weak transcription	Psoas Muscle	Psoas
5	chr10:52087600-52106600	Weak transcription	Stomach Mucosa	stomach
6	chr10:52087800-52107400	Weak transcription	NHEK	skin
7	chr10:52090800-52106800	Weak transcription	NHDF-Ad	bronchial
8	chr10:52094600-52109000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr10:52094800-52105600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:52095000-52109000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr10:52095200-52107200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr10:52095200-52119000	Weak transcription	Fetal Kidney	kidney
13	chr10:52095400-52106200	Weak transcription	HSMMtube	muscle
14	chr10:52095400-52118200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr10:52096400-52123000	Weak transcription	Small Intestine	intestine
16	chr10:52097600-52107000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr10:52102800-52107000	Weak transcription	Primary B cells from cord blood	blood
18	chr10:52103000-52106200	Strong transcription	K562	blood
19	chr10:52103000-52122400	Weak transcription	HUVEC	blood vessel
20	chr10:52103400-52106800	Weak transcription	Colon Smooth Muscle	Colon
21	chr10:52103600-52105800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr10:52103600-52106600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr10:52103600-52106800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr10:52103600-52107200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr10:52103600-52109000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr10:52103600-52118200	Weak transcription	Hela-S3	cervix
27	chr10:52103800-52105600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr10:52103800-52105800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr10:52103800-52106800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr10:52103800-52107000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:52103800-52107200	Weak transcription	Fetal Lung	lung
32	chr10:52103800-52108400	Weak transcription	HSMM	muscle
33	chr10:52103800-52108800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr10:52104000-52105600	Weak transcription	Fetal Intestine Large	intestine
35	chr10:52104000-52105800	Weak transcription	Colonic Mucosa	Colon
36	chr10:52104000-52105800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr10:52104000-52106000	Weak transcription	HepG2	liver
38	chr10:52104000-52106200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr10:52104000-52106200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr10:52104000-52106200	Weak transcription	Fetal Thymus	thymus
41	chr10:52104000-52106200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr10:52104000-52106400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr10:52104000-52106400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr10:52104000-52106400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr10:52104000-52106400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr10:52104000-52106400	Weak transcription	Placenta	Placenta
47	chr10:52104000-52106600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr10:52104000-52106600	Weak transcription	Fetal Intestine Small	intestine
49	chr10:52104000-52106800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr10:52104000-52106800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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