Variant report

Variant	rs11623869
Chromosome Location	chr14:103883633-103883634
allele	G/T
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	EBF1	chr14:103883299-103883674	GM12878	blood:	n/a	chr14:103883540-103883551
2	EP300	chr14:103883456-103883698	GM12878	blood:	n/a	n/a
3	MAX	chr14:103883453-103883660	H1-hESC	embryonic stem cell:	n/a	n/a
4	EBF1	chr14:103883330-103883724	GM12878	blood:	n/a	chr14:103883540-103883551

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:103876768..103879568-chr14:103882112..103883749,2	MCF-7	breast:
2	chr14:103799657..103801289-chr14:103882797..103884617,2	MCF-7	breast:

Variant related genes	Relation type
MARK3	TF binding region
ENSG00000244691	TF binding region
ENSG00000244691	Chromatin interaction
ENSG00000100664	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10129621	0.89[YRI][hapmap]
rs10130887	0.89[YRI][hapmap]
rs10133035	0.81[EUR][1000 genomes]
rs10134580	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1013650	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10138787	0.94[YRI][hapmap]
rs10139279	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10141120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10141388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10141433	0.88[EUR][1000 genomes]
rs10143247	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10145793	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10145934	0.89[YRI][hapmap]
rs10149860	0.89[YRI][hapmap]
rs10150072	0.84[EUR][1000 genomes]
rs1028613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11621037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11621510	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11622356	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11622835	0.93[JPT][hapmap]
rs11624367	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11626483	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11626787	0.80[EUR][1000 genomes]
rs11626905	0.86[JPT][hapmap]
rs11627052	0.83[CHD][hapmap];0.93[JPT][hapmap]
rs11628213	0.88[EUR][1000 genomes]
rs11628969	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12879085	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12888077	0.91[EUR][1000 genomes]
rs12889639	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12890750	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12898029	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1467561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs17617941	0.88[EUR][1000 genomes]
rs17679475	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1803283	1.00[CEU][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap]
rs1951392	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1961600	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1989565	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2010281	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2273700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2273703	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2296484	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs2403180	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28361338	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28369539	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28444993	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28496120	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28583452	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28626081	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34216351	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3742458	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3759579	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs3783394	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3783395	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3783402	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs3825566	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4900572	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4906321	0.91[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55723020	0.80[EUR][1000 genomes]
rs55859054	0.83[EUR][1000 genomes]
rs56365443	0.88[EUR][1000 genomes]
rs62006268	0.88[EUR][1000 genomes]
rs62007681	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007683	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62007684	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62007686	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62007687	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62007718	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62007719	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6575983	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6575984	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7140564	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7141712	0.89[YRI][hapmap]
rs7145113	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7146506	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7150317	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7152202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7154246	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7155014	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7155401	0.89[YRI][hapmap]
rs7156150	0.86[EUR][1000 genomes]
rs7158144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7158822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7160208	0.87[EUR][1000 genomes]
rs7160366	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72708854	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72708874	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72708893	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72710714	0.83[EUR][1000 genomes]
rs8013101	0.88[EUR][1000 genomes]
rs8015918	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8019578	0.84[EUR][1000 genomes]
rs9671911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049747	chr14:103126148-103955984	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
2	nsv534254	chr14:103470073-104023906	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv9168	chr14:103531729-103913306	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Bone mineral density	22504420	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11623869	CKB	Cis_1M	lymphoblastoid	RTeQTL
rs11623869	EIF5	cis	cerebellum	SCAN
rs11623869	MARK3	cis	cerebellum	SCAN
rs11623869	C14orf153	cis	cerebellum	SCAN
rs11623869	MARK3	cis	Thyroid	GTEx
rs11623869	BAG5	Cis_1M	lymphoblastoid	RTeQTL
rs11623869	KLC1	cis	parietal	SCAN
rs11623869	BAG5	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:103862000-103919400	Weak transcription	Colonic Mucosa	Colon
2	chr14:103868400-103883800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr14:103871000-103884400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr14:103872200-103883800	Strong transcription	Primary B cells from peripheral blood	blood
5	chr14:103874600-103884200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr14:103874600-103900800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr14:103875200-103888200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr14:103875200-103889200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr14:103875200-103893600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr14:103875400-103884200	Weak transcription	Psoas Muscle	Psoas
11	chr14:103875400-103884600	Weak transcription	Small Intestine	intestine
12	chr14:103875400-103887400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr14:103875400-103888600	Weak transcription	Gastric	stomach
14	chr14:103875400-103889600	Weak transcription	Colon Smooth Muscle	Colon
15	chr14:103875400-103892200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr14:103875400-103893600	Weak transcription	Brain Germinal Matrix	brain
17	chr14:103875600-103884600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr14:103875600-103893800	Weak transcription	Fetal Heart	heart
19	chr14:103875600-103894000	Weak transcription	Fetal Brain Male	brain
20	chr14:103875800-103889800	Weak transcription	Lung	lung
21	chr14:103876800-103887800	Weak transcription	Pancreas	Pancrea
22	chr14:103879000-103883800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr14:103879000-103892800	Weak transcription	Spleen	Spleen
24	chr14:103879000-103895200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr14:103879000-103914200	Weak transcription	Esophagus	oesophagus
26	chr14:103879000-103941400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr14:103879200-103887200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr14:103879600-103889400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr14:103879800-103887400	Weak transcription	HepG2	liver
30	chr14:103880200-103884200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr14:103880400-103894200	Weak transcription	Liver	Liver
32	chr14:103880400-103904600	Weak transcription	Fetal Kidney	kidney
33	chr14:103881000-103883800	Weak transcription	Primary T cells from cord blood	blood
34	chr14:103881000-103887000	Weak transcription	Thymus	Thymus
35	chr14:103881000-103889200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr14:103881000-103890600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr14:103881000-103900600	Weak transcription	Placenta	Placenta
38	chr14:103881200-103883800	Weak transcription	HUVEC	blood vessel
39	chr14:103882000-103884000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr14:103882000-103886000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr14:103882000-103887200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr14:103882200-103884600	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr14:103882400-103883800	Weak transcription	Primary B cells from cord blood	blood
44	chr14:103882600-103883800	Genic enhancers	NHDF-Ad	bronchial
45	chr14:103882600-103884200	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr14:103882600-103884200	Enhancers	Ovary	ovary
47	chr14:103882600-103885000	Enhancers	Adipose Nuclei	Adipose
48	chr14:103882600-103885200	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr14:103882600-103886800	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr14:103882800-103883800	Enhancers	H1 Cell Line	embryonic stem cell

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