Variant report

Variant	rs10838708
Chromosome Location	chr11:47441513-47441514
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47440779..47444528-chr11:47444653..47449178,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165916	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1057233	0.86[CHB][hapmap]
rs1064608	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10742803	0.87[ASN][1000 genomes]
rs10769258	0.83[ASW][hapmap];0.81[CHB][hapmap];0.84[GIH][hapmap];0.83[LWK][hapmap]
rs10769262	0.86[CHB][hapmap]
rs10838698	0.81[CHB][hapmap];0.84[GIH][hapmap]
rs10838699	0.81[CHB][hapmap]
rs10838704	0.85[ASN][1000 genomes]
rs10838706	0.85[ASN][1000 genomes]
rs11039212	0.83[ASW][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];0.81[MKK][hapmap]
rs11039219	0.85[ASN][1000 genomes]
rs11600581	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11604680	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs11605672	0.83[ASW][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.81[LWK][hapmap];0.80[MEX][hapmap]
rs12419692	0.90[CHB][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs12798346	0.90[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs1317149	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2053979	0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2053980	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2071304	0.86[CHB][hapmap]
rs2293577	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.87[ASN][1000 genomes]
rs2293578	0.95[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2293580	0.87[ASN][1000 genomes]
rs2868459	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs34958982	0.90[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs35496532	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3781624	0.86[ASN][1000 genomes]
rs3781625	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3781626	0.95[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3781627	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4752845	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs4752990	0.85[CHB][hapmap]
rs4752993	0.86[CHB][hapmap];0.86[GIH][hapmap]
rs4752994	0.86[CHB][hapmap]
rs4752999	0.95[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4992357	0.83[ASW][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.83[LWK][hapmap]
rs55927797	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs60075622	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6485753	0.86[CHB][hapmap]
rs7107726	0.85[ASN][1000 genomes]
rs7124681	0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap]
rs755553	0.95[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.85[ASN][1000 genomes]
rs755554	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs755555	0.85[ASN][1000 genomes]
rs7928842	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7937331	0.95[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs7940536	0.86[CHB][hapmap]
rs896816	0.83[ASW][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.83[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv825871	chr11:47376020-47457537	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv554210	chr11:47380593-47449544	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
8	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
9	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	23563607	GWAS catalog

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10838708	SPI1	cis	Lymphoblastoid	GTEx
rs10838708	C1QTNF4	cis	multi-tissue	Pritchard
rs10838708	PSMC3	cis	parietal	SCAN
rs10838708	NDUFS3	cis	cerebellum	SCAN
rs10838708	PTPRJ	cis	cerebellum	SCAN
rs10838708	MTCH2	cis	cerebellum	SCAN
rs10838708	SPI1	cis	multi-tissue	Pritchard
rs10838708	Hs.6637	cis	multi-tissue	Pritchard
rs10838708	C1QTNF4	cis	lymphoblastoid	seeQTL
rs10838708	SLC39A13	cis	cerebellum	SCAN
rs10838708		cis	Lymphoblastoid	GTEx
rs10838708	MADD	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47431000-47442000	Weak transcription	Primary B cells from cord blood	blood
2	chr11:47431200-47447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:47431600-47446400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr11:47432200-47446400	Strong transcription	Thymus	Thymus
5	chr11:47432400-47445800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr11:47432400-47446400	Weak transcription	Fetal Brain Male	brain
7	chr11:47432600-47445800	Strong transcription	Brain Anterior Caudate	brain
8	chr11:47432600-47446400	Strong transcription	Fetal Brain Female	brain
9	chr11:47432800-47446000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr11:47432800-47446200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr11:47432800-47446400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:47433200-47446200	Strong transcription	Fetal Thymus	thymus
13	chr11:47433400-47445800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr11:47434200-47445600	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr11:47434800-47446000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:47435000-47446000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:47435000-47446200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr11:47435000-47446200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr11:47435000-47446600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr11:47435200-47445800	Strong transcription	Liver	Liver
21	chr11:47435200-47446000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr11:47435200-47446400	Strong transcription	Primary T cells from cord blood	blood
23	chr11:47437400-47446400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr11:47437800-47446600	Strong transcription	Fetal Intestine Large	intestine
25	chr11:47438000-47445600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:47438000-47446200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:47438000-47446200	Strong transcription	Fetal Intestine Small	intestine
28	chr11:47438200-47441600	Weak transcription	Stomach Mucosa	stomach
29	chr11:47438200-47444200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr11:47438200-47446000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:47438200-47446000	Strong transcription	Adipose Nuclei	Adipose
32	chr11:47438200-47446200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr11:47438200-47446400	Weak transcription	Right Atrium	heart
34	chr11:47438200-47446600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:47438400-47445400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:47438400-47445800	Strong transcription	Fetal Stomach	stomach
37	chr11:47438400-47446000	Strong transcription	NHDF-Ad	bronchial
38	chr11:47438400-47446200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr11:47438600-47446000	Strong transcription	Brain Cingulate Gyrus	brain
40	chr11:47438600-47446000	Strong transcription	NHEK	skin
41	chr11:47438600-47446200	Strong transcription	Brain Germinal Matrix	brain
42	chr11:47438800-47444200	Strong transcription	Dnd41	blood
43	chr11:47438800-47445800	Strong transcription	Fetal Muscle Leg	muscle
44	chr11:47438800-47446000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:47438800-47446400	Strong transcription	Fetal Lung	lung
46	chr11:47439000-47441800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr11:47439000-47442600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr11:47439000-47445600	Strong transcription	Stomach Smooth Muscle	stomach
49	chr11:47439000-47445600	Strong transcription	K562	blood
50	chr11:47439000-47445800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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