Variant report

Variant	rs16846584
Chromosome Location	chr1:227064184-227064185
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	JUN	chr1:227063225-227064640	K562	blood:	n/a	chr1:227063805-227063816 chr1:227063809-227063817 chr1:227063807-227063819 chr1:227063781-227063792 chr1:227064566-227064576 chr1:227064105-227064114

No.	Distal block	Cell Line	Cell type
1	chr1:227056972..227060781-chr1:227061022..227064648,10	MCF-7	breast:
2	chr1:227063913..227065661-chr1:227075217..227077074,2	MCF-7	breast:
3	chr1:227061527..227064235-chr1:227072734..227074353,2	K562	blood:
4	chr1:227063874..227066086-chr1:227080166..227082122,2	K562	blood:
5	chr1:227064075..227066855-chr1:227067871..227070259,4	MCF-7	breast:
6	chr1:227057812..227060402-chr1:227061799..227065310,4	MCF-7	breast:
7	chr1:227062873..227064895-chr1:227127991..227129793,2	K562	blood:
8	chr1:227063887..227066680-chr1:227122260..227124831,2	K562	blood:

Variant related genes	Relation type
PSEN2	TF binding region
ENSG00000163050	Chromatin interaction
ENSG00000143801	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs4653780	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4766	chr1:227025954-227070961	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059000-227066800	Weak transcription	Aorta	Aorta
2	chr1:227059200-227069000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:227059400-227069600	Weak transcription	Primary B cells from cord blood	blood
4	chr1:227059600-227066000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:227059600-227068400	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:227059600-227069200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:227059600-227070200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:227059800-227064400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:227059800-227064400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:227059800-227064600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:227059800-227064600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:227059800-227064600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:227059800-227065000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:227059800-227067400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:227059800-227070200	Weak transcription	Osteobl	bone
16	chr1:227059800-227075600	Weak transcription	Brain Substantia Nigra	brain
17	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:227060000-227064600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:227060000-227064600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:227060000-227064600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:227060000-227065000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:227060000-227065000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:227060000-227065000	Weak transcription	HMEC	breast
24	chr1:227060000-227068200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:227060000-227068200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:227060000-227068400	Weak transcription	Brain Angular Gyrus	brain
27	chr1:227060000-227068800	Weak transcription	NHDF-Ad	bronchial
28	chr1:227060000-227069400	Weak transcription	Esophagus	oesophagus
29	chr1:227060000-227069600	Weak transcription	Right Atrium	heart
30	chr1:227060000-227069800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr1:227060000-227070000	Weak transcription	Small Intestine	intestine
32	chr1:227060000-227070600	Weak transcription	Fetal Brain Male	brain
33	chr1:227060200-227070200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:227060400-227066200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:227060400-227067000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:227060400-227068400	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:227060400-227069200	Weak transcription	GM12878-XiMat	blood
38	chr1:227060400-227073800	Weak transcription	HepG2	liver
39	chr1:227060400-227077600	Weak transcription	Brain Germinal Matrix	brain
40	chr1:227060600-227064200	Weak transcription	Adipose Nuclei	Adipose
41	chr1:227060600-227065000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:227060600-227067200	Weak transcription	Ovary	ovary
43	chr1:227060600-227067400	Weak transcription	NHLF	lung
44	chr1:227060600-227068400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:227060600-227070400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:227060600-227070400	Weak transcription	HUVEC	blood vessel
47	chr1:227060600-227077400	Weak transcription	Fetal Brain Female	brain
48	chr1:227061200-227069800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr1:227061600-227064600	Enhancers	Pancreas	Pancrea
50	chr1:227062000-227065800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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