Variant report

Variant	rs11666933
Chromosome Location	chr19:41862253-41862254
allele	A/G
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	CTCF	chr19:41856797-41862442	A549	lung:	n/a	chr19:41858550-41858559 chr19:41859909-41859918 chr19:41858546-41858559 chr19:41859459-41859472 chr19:41859906-41859924 chr19:41860035-41860053 chr19:41858544-41858562 chr19:41860037-41860050 chr19:41858547-41858557 chr19:41859906-41859919

No.	Distal block	Cell Line	Cell type
1	chr19:41817873..41820006-chr19:41861978..41863961,2	MCF-7	breast:
2	chr19:41825057..41828118-chr19:41860715..41862978,3	K562	blood:
3	chr19:41861604..41864575-chr19:41933607..41936595,2	MCF-7	breast:
4	chr19:41857382..41861361-chr19:41862121..41864311,4	MCF-7	breast:
5	chr19:41858489..41863412-chr19:41867730..41871601,11	K562	blood:
6	chr19:41861983..41864638-chr19:41901106..41902845,2	K562	blood:
7	chr19:41861756..41863483-chr19:41901345..41903943,2	K562	blood:
8	chr19:41773177..41775428-chr19:41862165..41864335,2	K562	blood:
9	chr19:41825452..41832651-chr19:41855170..41863054,16	K562	blood:
10	chr19:41856910..41863042-chr19:41867113..41873191,18	MCF-7	breast:
11	chr19:41859535..41862336-chr19:41931235..41934067,2	MCF-7	breast:

Variant related genes	Relation type
TGFB1	TF binding region
ENSG00000105323	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000123810	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000268475	Chromatin interaction
ENSG00000142039	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000077348	Chromatin interaction
ENSG00000177191	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1025497	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1046909	0.81[GIH][hapmap];0.88[MEX][hapmap]
rs11083616	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11083617	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11670143	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12462166	0.99[ASN][1000 genomes]
rs12983775	0.95[ASN][1000 genomes]
rs1549933	0.95[ASN][1000 genomes]
rs1800469	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1800470	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1963413	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1982072	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2231935	0.82[JPT][hapmap]
rs2241712	0.97[ASN][1000 genomes]
rs2241713	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241714	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2241715	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2317130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4803455	0.81[LWK][hapmap]
rs4803457	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803458	0.90[ASN][1000 genomes]
rs4803459	0.85[ASN][1000 genomes]
rs9797885	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1802868	chr19:41856886-41869392	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
2	nsv521311	chr19:41856886-41882712	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11666933	PSG2	cis	parietal	SCAN
rs11666933	ZNF45	cis	parietal	SCAN
rs11666933	LHB	cis	parietal	SCAN
rs11666933	CCDC114	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41859800-41868200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr19:41860000-41863800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:41860200-41862800	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr19:41860200-41864000	Weak transcription	Small Intestine	intestine
5	chr19:41860200-41864800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr19:41860200-41865000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr19:41860200-41869000	Weak transcription	Gastric	stomach
8	chr19:41860400-41862400	Enhancers	Lung	lung
9	chr19:41860400-41862600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:41860400-41862800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr19:41860400-41862800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:41860400-41862800	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr19:41860400-41862800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr19:41860400-41862800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr19:41860400-41863000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:41860400-41864400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:41860400-41864800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr19:41860400-41865800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr19:41860400-41868200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr19:41860400-41868600	Weak transcription	GM12878-XiMat	blood
21	chr19:41860400-41868800	Weak transcription	Hela-S3	cervix
22	chr19:41860400-41869000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:41860400-41869000	Weak transcription	Brain Angular Gyrus	brain
24	chr19:41860400-41869000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr19:41860400-41869200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr19:41860400-41869200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr19:41860400-41869200	Weak transcription	HSMMtube	muscle
28	chr19:41860400-41869200	Weak transcription	HUVEC	blood vessel
29	chr19:41860400-41869200	Weak transcription	NHDF-Ad	bronchial
30	chr19:41860400-41869200	Weak transcription	NHLF	lung
31	chr19:41860400-41869400	Weak transcription	Aorta	Aorta
32	chr19:41860400-41869400	Weak transcription	Ovary	ovary
33	chr19:41860600-41862400	Enhancers	Adipose Nuclei	Adipose
34	chr19:41860600-41863000	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr19:41860600-41863000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:41860600-41863000	Enhancers	Spleen	Spleen
37	chr19:41860600-41863200	Enhancers	Fetal Muscle Leg	muscle
38	chr19:41860600-41863600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr19:41860600-41864600	Enhancers	Primary hematopoietic stem cells	blood
40	chr19:41860600-41864600	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr19:41860600-41864800	Enhancers	Fetal Thymus	thymus
42	chr19:41860600-41866800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr19:41860600-41866800	Weak transcription	A549	lung
44	chr19:41860600-41868200	Weak transcription	Fetal Intestine Small	intestine
45	chr19:41860600-41868200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr19:41860600-41868400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr19:41860600-41868600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:41860600-41868800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr19:41860600-41869000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr19:41860600-41869200	Weak transcription	Muscle Satellite Cultured Cells	--

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