Variant report

Variant	rs10838709
Chromosome Location	chr11:47447346-47447347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47198368..47200069-chr11:47446814..47449315,2	MCF-7	breast:
2	chr11:47446295..47450524-chr11:47461441..47464685,6	MCF-7	breast:
3	chr11:47420268..47423188-chr11:47445332..47447348,2	K562	blood:
4	chr11:47290429..47293321-chr11:47445782..47448351,3	K562	blood:
5	chr11:47399004..47400770-chr11:47446343..47448819,3	K562	blood:
6	chr11:47290951..47293321-chr11:47445782..47448016,2	K562	blood:
7	chr11:47196939..47199221-chr11:47446629..47449473,2	K562	blood:

Variant related genes	Relation type
ENSG00000149182	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000252327	Chromatin interaction
ENSG00000264583	Chromatin interaction
ENSG00000165917	Chromatin interaction
ENSG00000066336	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10437655	0.88[EUR][1000 genomes]
rs10742802	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10742814	0.84[GIH][hapmap];0.95[JPT][hapmap]
rs10769263	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10769264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10838702	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10838705	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10838726	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10838732	0.95[JPT][hapmap]
rs11039221	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039225	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039244	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11039280	1.00[JPT][hapmap]
rs11606287	0.92[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs12292911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12361415	0.82[CHB][hapmap]
rs12577643	0.92[ASN][1000 genomes]
rs1377416	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1534576	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2203712	0.95[JPT][hapmap]
rs2242081	0.84[GIH][hapmap];0.95[JPT][hapmap]
rs2278890	0.92[CEU][hapmap]
rs2293576	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[ASN][1000 genomes]
rs2293579	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35032070	0.83[EUR][1000 genomes]
rs3740689	0.83[CHB][hapmap]
rs3740699	0.84[GIH][hapmap];0.84[JPT][hapmap]
rs3824869	0.88[CEU][hapmap]
rs4434960	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61897431	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6485758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6485763	0.84[GIH][hapmap];0.95[JPT][hapmap]
rs7103648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7104036	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7933019	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7947450	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7950696	0.95[JPT][hapmap]
rs874896	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs896817	0.83[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[GIH][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	nsv975328	chr11:47446815-47471052	Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10838709	MADD	cis	parietal	SCAN
rs10838709	C1QTNF4	cis	lymphoblastoid	seeQTL
rs10838709	C1QTNF4	cis	multi-tissue	Pritchard
rs10838709		cis	Lymphoblastoid	GTEx
rs10838709	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs10838709	MTCH2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47445800-47447400	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr11:47446200-47447800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
3	chr11:47446400-47447400	Flanking Active TSS	Brain Anterior Caudate	brain
4	chr11:47446400-47447400	Flanking Active TSS	HUVEC	blood vessel
5	chr11:47446400-47447600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:47446600-47447400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr11:47446600-47447400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
8	chr11:47446600-47447400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr11:47446600-47447400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:47446600-47447400	Flanking Active TSS	Brain Germinal Matrix	brain
11	chr11:47446600-47447400	Flanking Active TSS	Brain Hippocampus Middle	brain
12	chr11:47446600-47447400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:47446600-47447400	Flanking Active TSS	Colonic Mucosa	Colon
14	chr11:47446600-47447400	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr11:47446600-47447400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr11:47446600-47447400	Flanking Active TSS	HMEC	breast
17	chr11:47446600-47447600	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr11:47446600-47447600	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr11:47446600-47447800	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr11:47446600-47448000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
21	chr11:47446600-47448600	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr11:47446600-47449000	Active TSS	Psoas Muscle	Psoas
23	chr11:47446800-47447400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr11:47446800-47447400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr11:47446800-47447400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr11:47446800-47447400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr11:47446800-47447400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:47446800-47447400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
29	chr11:47446800-47447400	Flanking Active TSS	Brain Substantia Nigra	brain
30	chr11:47446800-47447400	Flanking Active TSS	Fetal Brain Male	brain
31	chr11:47446800-47447400	Flanking Active TSS	Fetal Thymus	thymus
32	chr11:47446800-47447400	Flanking Active TSS	Right Ventricle	heart
33	chr11:47446800-47447400	Flanking Active TSS	Stomach Mucosa	stomach
34	chr11:47446800-47447400	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr11:47446800-47447400	Flanking Active TSS	Thymus	Thymus
36	chr11:47446800-47447400	Flanking Active TSS	Osteobl	bone
37	chr11:47446800-47447600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr11:47446800-47447600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr11:47446800-47447600	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr11:47446800-47447600	Flanking Active TSS	Liver	Liver
41	chr11:47446800-47447600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr11:47446800-47448400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr11:47446800-47448400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:47446800-47448400	Active TSS	Small Intestine	intestine
45	chr11:47446800-47448600	Active TSS	H9 Cell Line	embryonic stem cell
46	chr11:47446800-47448600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr11:47447000-47447400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr11:47447000-47447400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr11:47447000-47447400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr11:47447000-47447400	Flanking Active TSS	Colon Smooth Muscle	Colon

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