Variant report

Variant	rs33053
Chromosome Location	chr3:159601763-159601764
allele	C/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	MXI1	chr3:159598667-159601772	SK-N-SH	brain:	n/a	n/a
2	RAD21	chr3:159599160-159603476	SK-N-SH	brain:	n/a	chr3:159600668-159600682 chr3:159600519-159600531 chr3:159601277-159601291
3	TCF12	chr3:159600457-159601777	SK-N-SH	brain:	n/a	n/a
4	EP300	chr3:159598924-159602156	SK-N-SH	brain:	n/a	chr3:159599050-159599064 chr3:159601375-159601385 chr3:159601465-159601474

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:159546081..159548652-chr3:159599760..159602729,2	MCF-7	breast:

Variant related genes	Relation type
SCHIP1	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1009058	0.84[CEU][hapmap]
rs1675496	0.84[CEU][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs33055	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.95[ASN][1000 genomes]
rs33057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs33058	0.94[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];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	nsv877698	chr3:159583518-159640152	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv997776	chr3:159585097-159668421	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159588200-159605200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:159590800-159617600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:159593400-159605400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:159594000-159606600	Weak transcription	Fetal Kidney	kidney
5	chr3:159596200-159613200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:159597000-159605800	Enhancers	Brain Angular Gyrus	brain
7	chr3:159598200-159602000	Enhancers	HMEC	breast
8	chr3:159598600-159601800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:159598800-159602800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:159599000-159601800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:159599200-159601800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:159599200-159601800	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr3:159599200-159603200	Enhancers	HUVEC	blood vessel
14	chr3:159599400-159602000	Enhancers	NHLF	lung
15	chr3:159599400-159603600	Enhancers	Colon Smooth Muscle	Colon
16	chr3:159599600-159601800	Enhancers	Fetal Muscle Leg	muscle
17	chr3:159599800-159609400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:159599800-159620400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:159600000-159610200	Weak transcription	Esophagus	oesophagus
20	chr3:159600000-159610200	Weak transcription	A549	lung
21	chr3:159600400-159602000	Enhancers	NHEK	skin
22	chr3:159600400-159605000	Weak transcription	Aorta	Aorta
23	chr3:159600400-159605400	Weak transcription	Adipose Nuclei	Adipose
24	chr3:159600800-159602000	Enhancers	Stomach Smooth Muscle	stomach
25	chr3:159600800-159603800	Enhancers	Brain Anterior Caudate	brain
26	chr3:159600800-159604000	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr3:159600800-159604200	Enhancers	Fetal Heart	heart
28	chr3:159600800-159609400	Weak transcription	Fetal Brain Female	brain
29	chr3:159601000-159601800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:159601000-159603800	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr3:159601000-159606000	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr3:159601000-159610200	Weak transcription	Placenta	Placenta
33	chr3:159601200-159602000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:159601200-159604200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr3:159601200-159604400	Enhancers	Rectal Smooth Muscle	rectum
36	chr3:159601200-159607200	Enhancers	Brain Hippocampus Middle	brain
37	chr3:159601200-159609800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:159601200-159609800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:159601200-159609800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:159601200-159610000	Weak transcription	Spleen	Spleen
41	chr3:159601200-159610200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:159601200-159615200	Weak transcription	Fetal Intestine Small	intestine
43	chr3:159601400-159601800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:159601400-159601800	Enhancers	HSMM	muscle
45	chr3:159601400-159602400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:159601400-159602600	Weak transcription	Fetal Stomach	stomach
47	chr3:159601400-159602600	Weak transcription	Left Ventricle	heart
48	chr3:159601400-159602600	Weak transcription	Psoas Muscle	Psoas
49	chr3:159601400-159602600	Weak transcription	Right Atrium	heart
50	chr3:159601400-159602600	Weak transcription	Right Ventricle	heart

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