Variant report

Variant	rs480846
Chromosome Location	chr11:102345234-102345235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr11:102344812-102345874	GM12878	blood:	n/a	n/a
2	WRNIP1	chr11:102345153-102345571	GM12878	blood:	n/a	n/a
3	ZNF143	chr11:102345072-102345636	GM12878	blood:	n/a	n/a
4	ATF2	chr11:102345044-102345741	GM12878	blood:	n/a	n/a
5	STAT1	chr11:102345088-102345255	GM12878	blood:	n/a	n/a
6	NFIC	chr11:102344878-102345756	GM12878	blood:	n/a	n/a
7	POLR2A	chr11:102344422-102345794	Raji	blood:	n/a	n/a
8	FOXM1	chr11:102344953-102345826	GM12878	blood:	n/a	n/a
9	POU2F2	chr11:102344986-102345883	GM12878	blood:	n/a	n/a
10	FOXM1	chr11:102344982-102345802	GM12878	blood:	n/a	n/a
11	SP1	chr11:102344945-102345761	GM12878	blood:	n/a	n/a
12	SP1	chr11:102345031-102345750	GM12878	blood:	n/a	n/a
13	ATF2	chr11:102344939-102345792	GM12878	blood:	n/a	n/a
14	MTA3	chr11:102344689-102345824	GM12878	blood:	n/a	n/a
15	BHLHE40	chr11:102344985-102345744	GM12878	blood:	n/a	n/a
16	EP300	chr11:102344974-102345681	GM12878	blood:	n/a	n/a
17	STAT3	chr11:102345014-102345671	GM12878	blood:	n/a	n/a
18	CUX1	chr11:102345036-102345744	GM12878	blood:	n/a	n/a
19	RCOR1	chr11:102344815-102345671	GM12878	blood:	n/a	n/a
20	CREB1	chr11:102344908-102345786	GM12878	blood:	n/a	n/a
21	CHD2	chr11:102344717-102345763	GM12878	blood:	n/a	n/a
22	PBX3	chr11:102345096-102345323	GM12878	blood:	n/a	n/a
23	BCLAF1	chr11:102345097-102345825	GM12878	blood:	n/a	n/a
24	EP300	chr11:102345013-102345344	GM12878	blood:	n/a	n/a
25	CREB1	chr11:102344897-102345775	GM12878	blood:	n/a	n/a
26	TBL1XR1	chr11:102344921-102345767	GM12878	blood:	n/a	n/a
27	BCLAF1	chr11:102345014-102345761	GM12878	blood:	n/a	n/a
28	MAZ	chr11:102345135-102345730	GM12878	blood:	n/a	n/a
29	MAX	chr11:102344985-102345734	GM12878	blood:	n/a	n/a
30	EP300	chr11:102344958-102345826	GM12878	blood:	n/a	n/a
31	PAX5	chr11:102345064-102345695	GM12878	blood:	n/a	n/a
32	PAX5	chr11:102345043-102345847	GM12878	blood:	n/a	n/a
33	POU2F2	chr11:102345030-102345357	GM12878	blood:	n/a	n/a
34	RELA	chr11:102345045-102345743	GM19099	blood:	n/a	n/a
35	PAX5	chr11:102345056-102345553	GM12878	blood:	n/a	n/a
36	TCF3	chr11:102345073-102345306	GM12878	blood:	n/a	n/a
37	SMC3	chr11:102344895-102345683	GM12878	blood:	n/a	n/a
38	POU2F2	chr11:102345077-102345722	GM12891	blood:	n/a	n/a
39	RELA	chr11:102344573-102345818	GM12891	blood:	n/a	n/a
40	TBP	chr11:102345056-102345755	GM12878	blood:	n/a	n/a
41	RUNX3	chr11:102344712-102345879	GM12878	blood:	n/a	n/a
42	TCF3	chr11:102345072-102345806	GM12878	blood:	n/a	n/a
43	EBF1	chr11:102345220-102345677	GM12878	blood:	n/a	n/a
44	MXI1	chr11:102345016-102345743	GM12878	blood:	n/a	n/a
45	ZNF384	chr11:102345233-102345743	GM12878	blood:	n/a	n/a
46	EP300	chr11:102344958-102345767	GM12878	blood:	n/a	n/a
47	NFIC	chr11:102344915-102345796	GM12878	blood:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:102323431..102326231-chr11:102344415..102346737,2	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM123	TF binding region
ENSG00000255337	Chromatin interaction
ENSG00000152558	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2019777	1.00[CEU][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2156530	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs490860	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs518851	1.00[CEU][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs530227	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs539751	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs548841	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs548974	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs557747	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs558679	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs589271	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs602271	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs621010	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs650411	0.93[EUR][1000 genomes]
rs651853	1.00[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs652329	0.86[EUR][1000 genomes]
rs666042	0.82[EUR][1000 genomes]
rs683933	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3514195	chr11:102118479-102348362	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv3514197	chr11:102118479-102348362	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers 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	13 gene(s)	inside rSNPs	diseases
3	nsv1035567	chr11:102264516-102431607	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv898334	chr11:102272884-102353192	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv469990	chr11:102335609-102413943	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv556150	chr11:102335609-102415859	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv468854	chr11:102336617-102413943	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv556151	chr11:102336617-102413943	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs480846	DYNC2H1	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102334800-102345600	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr11:102338000-102347000	Weak transcription	Small Intestine	intestine
3	chr11:102339000-102345800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr11:102339000-102347400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:102339200-102345600	Enhancers	Primary T cells fromperipheralblood	blood
6	chr11:102339800-102347000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:102340600-102346800	Weak transcription	A549	lung
8	chr11:102340800-102345600	Weak transcription	Spleen	Spleen
9	chr11:102340800-102347000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr11:102340800-102347200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr11:102340800-102347600	Weak transcription	Lung	lung
12	chr11:102341000-102346800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:102341000-102347400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:102341000-102359600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:102341200-102345400	Enhancers	Primary T cells from cord blood	blood
16	chr11:102341400-102345600	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr11:102341800-102347200	Weak transcription	Dnd41	blood
18	chr11:102342000-102347000	Weak transcription	Thymus	Thymus
19	chr11:102342000-102347200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr11:102342000-102347400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr11:102342000-102347400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr11:102342000-102347400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:102342000-102347400	Weak transcription	Fetal Heart	heart
24	chr11:102342400-102347000	Weak transcription	NHEK	skin
25	chr11:102342400-102347200	Weak transcription	Fetal Thymus	thymus
26	chr11:102342400-102347400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr11:102342400-102347400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:102342600-102346800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:102342800-102347000	Weak transcription	HMEC	breast
30	chr11:102342800-102347200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr11:102343000-102346200	Weak transcription	Liver	Liver
32	chr11:102344000-102345400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr11:102344000-102345600	Enhancers	Stomach Mucosa	stomach
34	chr11:102344200-102346000	Enhancers	Primary B cells from peripheral blood	blood
35	chr11:102344400-102345600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr11:102344400-102346200	Enhancers	Primary B cells from cord blood	blood
37	chr11:102344400-102346800	Enhancers	HepG2	liver
38	chr11:102344600-102347000	Weak transcription	K562	blood
39	chr11:102344600-102348000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:102344600-102348200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr11:102344800-102345600	Flanking Active TSS	GM12878-XiMat	blood
42	chr11:102345000-102345400	Weak transcription	Colon Smooth Muscle	Colon
43	chr11:102345000-102346200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr11:102345000-102346200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr11:102345000-102347000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr11:102345000-102347200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr11:102345000-102347200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr11:102345000-102349200	Weak transcription	Colonic Mucosa	Colon
49	chr11:102345000-102351600	Weak transcription	Gastric	stomach
50	chr11:102345200-102345400	Enhancers	Fetal Lung	lung

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