Variant report

Variant	rs11005290
Chromosome Location	chr10:52107120-52107121
allele	C/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	POLR2A	chr10:52107036-52107604	GM12892	blood:	n/a	n/a
2	RELA	chr10:52107114-52107858	GM19099	blood:	n/a	n/a
3	POLR2A	chr10:52107003-52107776	GM12892	blood:	n/a	n/a
4	CUX1	chr10:52106973-52107637	GM12878	blood:	n/a	n/a
5	STAT3	chr10:52106932-52107511	GM12878	blood:	n/a	n/a
6	NFIC	chr10:52106977-52107622	GM12878	blood:	n/a	chr10:52107482-52107499 chr10:52107483-52107499
7	RELA	chr10:52107077-52107698	GM18505	blood:	n/a	n/a
8	POLR2A	chr10:52105913-52107565	K562	blood:	n/a	n/a
9	EP300	chr10:52106894-52107642	GM12878	blood:	n/a	chr10:52107460-52107474
10	POLR2A	chr10:52107108-52107814	GM12892	blood:	n/a	n/a
11	RELA	chr10:52106944-52107828	GM12891	blood:	n/a	n/a
12	EBF1	chr10:52106688-52108009	GM12878	blood:	n/a	chr10:52107421-52107432
13	RELA	chr10:52106872-52107656	GM15510	blood:	n/a	n/a
14	ATF2	chr10:52107026-52107665	GM12878	blood:	n/a	n/a
15	POLR2A	chr10:52107000-52107976	GM12878	blood:	n/a	n/a
16	MXI1	chr10:52106995-52107587	GM12878	blood:	n/a	n/a
17	CUX1	chr10:52106859-52107486	K562	blood:	n/a	n/a
18	BCLAF1	chr10:52107061-52107659	GM12878	blood:	n/a	n/a
19	SPI1	chr10:52107065-52107472	HL-60	blood:	n/a	chr10:52107285-52107294 chr10:52107282-52107295
20	POLR2A	chr10:52107085-52108074	GM12878	blood:	n/a	n/a
21	RFX5	chr10:52107118-52107291	GM12878	blood:	n/a	n/a
22	MAX	chr10:52106799-52107508	GM12878	blood:	n/a	n/a
23	BHLHE40	chr10:52107092-52107616	GM12878	blood:	n/a	n/a
24	SPI1	chr10:52106963-52107774	GM12878	blood:	n/a	chr10:52107567-52107574 chr10:52107285-52107294 chr10:52107282-52107295
25	RELA	chr10:52106820-52107689	GM12878	blood:	n/a	n/a
26	SPI1	chr10:52107069-52107528	HL-60	blood:	n/a	chr10:52107285-52107294 chr10:52107282-52107295
27	ATF2	chr10:52106973-52107749	GM12878	blood:	n/a	n/a
28	MTA3	chr10:52106722-52108069	GM12878	blood:	n/a	n/a
29	RUNX3	chr10:52107100-52108028	GM12878	blood:	n/a	n/a
30	SMC3	chr10:52107079-52107593	GM12878	blood:	n/a	chr10:52107210-52107217
31	RELA	chr10:52107107-52107948	GM18951	blood:	n/a	n/a
32	EBF1	chr10:52106980-52107584	GM12878	blood:	n/a	chr10:52107421-52107432
33	EBF1	chr10:52106958-52107657	GM12878	blood:	n/a	chr10:52107421-52107432
34	POLR2A	chr10:52106746-52107593	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:52105040..52107754-chr10:52130504..52132718,2	MCF-7	breast:

Variant related genes	Relation type
SGMS1	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11005215	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12240352	0.84[ASN][1000 genomes]
rs1344848	0.92[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs1436212	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1436214	0.83[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs17785945	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1898196	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1898197	0.84[EUR][1000 genomes]
rs2060561	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60381888	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7069978	0.81[ASN][1000 genomes]
rs7911266	0.94[CEU][hapmap];0.92[JPT][hapmap];0.85[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11005290	SGMS1	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52087200-52107400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr10:52087800-52107400	Weak transcription	NHEK	skin
3	chr10:52094600-52109000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr10:52095000-52109000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr10:52095200-52107200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr10:52095200-52119000	Weak transcription	Fetal Kidney	kidney
7	chr10:52095400-52118200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr10:52096400-52123000	Weak transcription	Small Intestine	intestine
9	chr10:52103000-52122400	Weak transcription	HUVEC	blood vessel
10	chr10:52103600-52107200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr10:52103600-52109000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr10:52103600-52118200	Weak transcription	Hela-S3	cervix
13	chr10:52103800-52107200	Weak transcription	Fetal Lung	lung
14	chr10:52103800-52108400	Weak transcription	HSMM	muscle
15	chr10:52103800-52108800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr10:52104000-52107200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr10:52104000-52107200	Weak transcription	Brain Anterior Caudate	brain
18	chr10:52104000-52107200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr10:52104000-52107200	Weak transcription	Esophagus	oesophagus
20	chr10:52104000-52107200	Weak transcription	Ovary	ovary
21	chr10:52104000-52107200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr10:52104000-52107400	Weak transcription	Right Ventricle	heart
23	chr10:52104000-52107400	Weak transcription	Thymus	Thymus
24	chr10:52104000-52107400	Weak transcription	Spleen	Spleen
25	chr10:52104000-52107800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr10:52104000-52107800	Weak transcription	Fetal Stomach	stomach
27	chr10:52104000-52108400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr10:52104000-52108800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr10:52104000-52108800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr10:52104000-52108800	Weak transcription	Fetal Muscle Leg	muscle
31	chr10:52104000-52109000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr10:52104000-52109200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr10:52104000-52109200	Weak transcription	Gastric	stomach
34	chr10:52104000-52115000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr10:52104000-52115000	Weak transcription	Lung	lung
36	chr10:52104000-52116400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr10:52104000-52118200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr10:52104000-52123200	Weak transcription	Aorta	Aorta
39	chr10:52104000-52134000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr10:52104000-52141400	Weak transcription	Pancreas	Pancrea
41	chr10:52104200-52107200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr10:52104200-52107200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr10:52104200-52107200	Weak transcription	Osteobl	bone
44	chr10:52104200-52108800	Weak transcription	Primary T cells from cord blood	blood
45	chr10:52104200-52108800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr10:52104200-52108800	Weak transcription	A549	lung
47	chr10:52104200-52109000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr10:52104200-52110000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr10:52104200-52110800	Weak transcription	Liver	Liver
50	chr10:52104200-52111600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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