Variant report

Variant	rs12973666
Chromosome Location	chr19:41289397-41289398
allele	C/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	POLR2A	chr19:41288920-41290834	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41280731..41296556-chr19:41299561..41307605,30	MCF-7	breast:
2	chr19:41267351..41269618-chr19:41286663..41289461,3	K562	blood:
3	chr19:41286626..41290245-chr19:41304017..41305752,4	K562	blood:
4	chr19:41267351..41269459-chr19:41286783..41289461,2	K562	blood:

Variant related genes	Relation type
RAB4B	TF binding region
ENSG00000268797	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000269858	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12151282	0.84[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs17726276	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279011	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305797	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs35858034	0.87[ASN][1000 genomes]
rs3733829	0.82[JPT][hapmap]
rs3736329	0.82[JPT][hapmap]
rs4802091	0.82[JPT][hapmap]
rs4803369	0.82[JPT][hapmap]
rs7245595	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs7254192	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7937	0.85[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12973666	CEACAM21	cis	lymphoblastoid	seeQTL
rs12973666	EGLN2	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41285000-41292400	Weak transcription	Ovary	ovary
2	chr19:41285000-41303800	Weak transcription	Small Intestine	intestine
3	chr19:41285000-41304000	Weak transcription	Psoas Muscle	Psoas
4	chr19:41285200-41289800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:41285200-41289800	Weak transcription	Adipose Nuclei	Adipose
6	chr19:41285200-41289800	Weak transcription	Brain Angular Gyrus	brain
7	chr19:41285200-41289800	Weak transcription	Brain Substantia Nigra	brain
8	chr19:41285200-41289800	Weak transcription	Fetal Muscle Leg	muscle
9	chr19:41285200-41290200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr19:41285200-41291600	Weak transcription	Esophagus	oesophagus
11	chr19:41285200-41292200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr19:41285200-41292400	Weak transcription	Brain Germinal Matrix	brain
13	chr19:41285200-41292400	Weak transcription	Left Ventricle	heart
14	chr19:41285200-41295600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:41285200-41295600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr19:41285200-41298000	Weak transcription	Fetal Lung	lung
17	chr19:41285200-41303200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:41285200-41303400	Weak transcription	Pancreas	Pancrea
19	chr19:41285200-41303600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr19:41285200-41303800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr19:41285200-41304000	Weak transcription	HSMM	muscle
22	chr19:41285400-41289400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:41285400-41289600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:41285400-41289800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:41285400-41289800	Weak transcription	Fetal Intestine Large	intestine
26	chr19:41285400-41290200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr19:41285400-41291000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:41285400-41291400	Weak transcription	A549	lung
29	chr19:41285400-41291600	Weak transcription	Fetal Brain Female	brain
30	chr19:41285400-41292200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr19:41285400-41292200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:41285400-41292200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:41285400-41292400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr19:41285400-41292600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr19:41285400-41292600	Weak transcription	Colonic Mucosa	Colon
36	chr19:41285400-41293400	Weak transcription	Liver	Liver
37	chr19:41285400-41295600	Weak transcription	Right Ventricle	heart
38	chr19:41285400-41296800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr19:41285400-41297000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:41285400-41297400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:41285400-41297400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr19:41285400-41297600	Weak transcription	Stomach Mucosa	stomach
43	chr19:41285400-41297800	Weak transcription	NHDF-Ad	bronchial
44	chr19:41285400-41298000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr19:41285400-41302400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr19:41285400-41303400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr19:41285400-41303400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr19:41285400-41303400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr19:41285400-41303400	Weak transcription	Colon Smooth Muscle	Colon
50	chr19:41285400-41303400	Weak transcription	HMEC	breast

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