Variant report

Variant	rs11673466
Chromosome Location	chr19:18401142-18401143
allele	A/C
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	EP300	chr19:18400964-18401685	GM12878	blood:	n/a	n/a
2	TCF3	chr19:18401098-18401599	GM12878	blood:	n/a	chr19:18401323-18401336
3	EBF1	chr19:18401002-18401599	GM12878	blood:	n/a	chr19:18401359-18401368 chr19:18401359-18401369 chr19:18401358-18401369
4	RELA	chr19:18401130-18401656	GM18505	blood:	n/a	n/a
5	RCOR1	chr19:18400980-18401651	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:18401139-18401567	GM12878	blood:	n/a	n/a
7	RELA	chr19:18400943-18401621	GM12878	blood:	n/a	n/a
8	ATF2	chr19:18401021-18401744	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:18401132-18401677	GM12891	blood:	n/a	n/a
10	MEF2C	chr19:18401088-18401657	GM12878	blood:	n/a	n/a
11	BATF	chr19:18401050-18401628	GM12878	blood:	n/a	n/a
12	USF2	chr19:18401142-18401421	GM12878	blood:	n/a	n/a
13	CHD2	chr19:18401084-18401585	GM12878	blood:	n/a	n/a
14	POU2F2	chr19:18400942-18401636	GM12891	blood:	n/a	chr19:18401301-18401313 chr19:18401184-18401196
15	YY1	chr19:18401105-18401575	GM12878	blood:	n/a	chr19:18401501-18401510
16	ELF1	chr19:18401047-18401545	GM12878	blood:	n/a	n/a
17	PAX5	chr19:18400941-18401644	GM12878	blood:	n/a	n/a
18	EBF1	chr19:18401042-18401651	GM12878	blood:	n/a	chr19:18401359-18401368 chr19:18401359-18401369 chr19:18401358-18401369
19	STAT5A	chr19:18401042-18401664	GM12878	blood:	n/a	chr19:18401299-18401311
20	MAX	chr19:18401099-18401499	NB4	blood:	n/a	chr19:18401185-18401195
21	POLR2A	chr19:18400597-18401245	K562	blood:	n/a	n/a
22	TCF12	chr19:18401090-18401562	GM12878	blood:	n/a	n/a
23	HDAC2	chr19:18400930-18401270	K562	blood:	n/a	n/a
24	MYC	chr19:18401139-18401504	NB4	blood:	n/a	chr19:18401185-18401195
25	POLR2A	chr19:18401054-18401444	K562	blood:	n/a	n/a
26	BHLHE40	chr19:18400984-18401622	GM12878	blood:	n/a	n/a
27	NFIC	chr19:18400953-18401727	GM12878	blood:	n/a	n/a
28	RELA	chr19:18401042-18401619	GM10847	blood:	n/a	n/a
29	BCL11A	chr19:18401010-18401661	GM12878	blood:	n/a	chr19:18401501-18401514
30	MAZ	chr19:18401043-18401630	GM12878	blood:	n/a	chr19:18401185-18401195
31	YY1	chr19:18401131-18401326	K562	blood:	n/a	n/a
32	MEF2A	chr19:18401057-18401683	GM12878	blood:	n/a	n/a
33	POU2F2	chr19:18401063-18401592	GM12878	blood:	n/a	chr19:18401301-18401313 chr19:18401184-18401196
34	EP300	chr19:18401119-18401683	GM12878	blood:	n/a	n/a
35	FOXM1	chr19:18400850-18401754	GM12878	blood:	n/a	n/a
36	EP300	chr19:18401136-18401695	GM12878	blood:	n/a	n/a
37	YY1	chr19:18401009-18401567	GM12892	blood:	n/a	chr19:18401501-18401510
38	TBL1XR1	chr19:18400844-18401658	GM12878	blood:	n/a	n/a
39	MXI1	chr19:18401130-18401598	GM12878	blood:	n/a	n/a
40	BCLAF1	chr19:18400865-18401670	GM12878	blood:	n/a	chr19:18401501-18401514
41	RCOR1	chr19:18401088-18401413	K562	blood:	n/a	n/a
42	ATF2	chr19:18400932-18401662	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:18401017-18401649	GM12892	blood:	n/a	n/a
44	JUND	chr19:18401050-18401250	K562	blood:	n/a	chr19:18401184-18401193
45	MAX	chr19:18400896-18401308	K562	blood:	n/a	chr19:18401185-18401195
46	SP1	chr19:18400964-18401656	GM12878	blood:	n/a	chr19:18401299-18401313 chr19:18401188-18401201
47	BCL3	chr19:18400901-18401639	GM12878	blood:	n/a	chr19:18401501-18401514
48	IRF1	chr19:18400791-18401170	K562	blood:	n/a	n/a
49	STAT3	chr19:18400964-18401622	GM12878	blood:	n/a	chr19:18401299-18401311
50	RELA	chr19:18401142-18401605	GM15510	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18400699..18403651-chr19:18419852..18422642,3	MCF-7	breast:
2	chr19:18312262..18317051-chr19:18400963..18403805,6	K562	blood:
3	chr19:18397375..18399268-chr19:18401136..18404109,3	MCF-7	breast:
4	chr19:18399894..18406849-chr19:18524216..18528146,7	K562	blood:
5	chr19:18400747..18403330-chr19:18449390..18451589,2	MCF-7	breast:
6	chr19:18383365..18408325-chr19:18518460..18533256,66	K562	blood:
7	chr19:18399345..18407720-chr19:18430417..18436364,18	MCF-7	breast:
8	chr19:18397948..18402412-chr19:18484415..18487037,3	K562	blood:

Variant related genes	Relation type
RPL39P38	TF binding region
ENSG00000130511	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000130520	Chromatin interaction
ENSG00000221167	Chromatin interaction
ENSG00000268650	Chromatin interaction
ENSG00000130517	Chromatin interaction
ENSG00000105649	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11668229	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34503849	1.00[ASN][1000 genomes]
rs8102397	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription 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 miRNA target site	204 gene(s)	inside rSNPs	diseases
2	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv911253	chr19:18240127-18418044	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
5	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS 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	162 gene(s)	inside rSNPs	diseases
6	nsv911269	chr19:18351674-18418044	Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
7	nsv911270	chr19:18351674-18422364	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
8	nsv911271	chr19:18362940-18453124	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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	135 gene(s)	inside rSNPs	diseases
9	nsv828472	chr19:18377725-18404131	Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	117 gene(s)	inside rSNPs	diseases
10	esv1833305	chr19:18378219-18408222	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	117 gene(s)	inside rSNPs	diseases
11	nsv911272	chr19:18378219-18439383	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
12	nsv911273	chr19:18386798-18454825	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	134 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11673466	CTD-3137H5.1	cis	Whole Blood	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18393800-18401200	Weak transcription	Right Atrium	heart
2	chr19:18393800-18402000	Weak transcription	Aorta	Aorta
3	chr19:18394000-18401200	Weak transcription	Brain Hippocampus Middle	brain
4	chr19:18394000-18401400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:18394000-18401400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr19:18394000-18402000	Weak transcription	Brain Anterior Caudate	brain
7	chr19:18394000-18402800	Weak transcription	Gastric	stomach
8	chr19:18394400-18402000	Weak transcription	Pancreas	Pancrea
9	chr19:18394400-18402000	Weak transcription	Right Ventricle	heart
10	chr19:18394600-18402200	Weak transcription	Psoas Muscle	Psoas
11	chr19:18396000-18402600	Weak transcription	Small Intestine	intestine
12	chr19:18396200-18402600	Weak transcription	Liver	Liver
13	chr19:18396400-18401400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr19:18397800-18401400	Enhancers	Primary T cells fromperipheralblood	blood
15	chr19:18397800-18402000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr19:18397800-18402000	Weak transcription	HSMMtube	muscle
17	chr19:18397800-18402200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:18398400-18402200	Enhancers	Fetal Thymus	thymus
19	chr19:18398800-18402000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:18399000-18401400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr19:18399000-18402000	Enhancers	Primary B cells from peripheral blood	blood
22	chr19:18399000-18402000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr19:18399000-18402000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:18399200-18401200	Weak transcription	Fetal Heart	heart
25	chr19:18399200-18402000	Enhancers	Primary B cells from cord blood	blood
26	chr19:18399400-18401200	Weak transcription	Colon Smooth Muscle	Colon
27	chr19:18399400-18401400	Weak transcription	Fetal Intestine Large	intestine
28	chr19:18399400-18402000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr19:18399400-18402000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:18399400-18402000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr19:18399400-18402200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:18399400-18402200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:18399400-18402200	Weak transcription	Fetal Kidney	kidney
34	chr19:18399400-18402400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:18399600-18401200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr19:18399600-18402000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr19:18399600-18402200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr19:18399600-18402200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:18399800-18402000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:18399800-18402000	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr19:18400000-18402000	Enhancers	Primary hematopoietic stem cells	blood
42	chr19:18400200-18401400	Enhancers	Primary T cells from cord blood	blood
43	chr19:18400200-18402000	Enhancers	Placenta	Placenta
44	chr19:18400200-18402400	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr19:18400400-18401200	Enhancers	H9 Cell Line	embryonic stem cell
46	chr19:18400400-18402000	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr19:18400400-18402200	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr19:18400400-18402400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:18400600-18401200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr19:18400600-18401200	Enhancers	Ovary	ovary

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