Variant report

Variant	rs17021374
Chromosome Location	chr3:28377116-28377117
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	chr3:28375882-28377603	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:28373806..28377718-chr3:28387703..28390768,4	MCF-7	breast:

Variant related genes	Relation type
AZI2	TF binding region
ENSG00000206559	Chromatin interaction
ENSG00000163512	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17021177	0.83[YRI][hapmap]
rs17021318	0.83[YRI][hapmap]
rs17021331	0.83[YRI][hapmap]
rs17021333	0.83[YRI][hapmap]
rs17021335	0.83[YRI][hapmap]
rs17021341	0.83[YRI][hapmap]
rs17021351	0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17021353	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17021360	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17021368	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17021369	0.83[YRI][hapmap]
rs17021371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17021372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17021505	0.83[YRI][hapmap]
rs17029779	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7639746	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7643610	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7651491	1.00[AMR][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	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28317600-28380000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:28317600-28389400	Weak transcription	Esophagus	oesophagus
3	chr3:28343800-28383800	Weak transcription	Aorta	Aorta
4	chr3:28349800-28389400	Weak transcription	Gastric	stomach
5	chr3:28358600-28386400	Weak transcription	Thymus	Thymus
6	chr3:28358800-28389000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:28359600-28377200	Weak transcription	Brain Anterior Caudate	brain
8	chr3:28360400-28383800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:28360400-28387400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:28361600-28382200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:28362800-28382400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:28362800-28387800	Weak transcription	HUVEC	blood vessel
13	chr3:28363200-28377200	Weak transcription	Fetal Kidney	kidney
14	chr3:28363600-28389000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:28363800-28380000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:28363800-28389600	Weak transcription	Spleen	Spleen
17	chr3:28364000-28388400	Weak transcription	Fetal Brain Female	brain
18	chr3:28364800-28382400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:28365400-28383800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:28365400-28389400	Weak transcription	Lung	lung
21	chr3:28366000-28388600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:28366200-28378000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr3:28366200-28389400	Weak transcription	Colonic Mucosa	Colon
24	chr3:28366400-28389200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:28366800-28379000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:28367000-28384200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:28367000-28388800	Weak transcription	Brain Angular Gyrus	brain
28	chr3:28367000-28389000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:28367200-28379000	Weak transcription	HSMMtube	muscle
30	chr3:28367200-28384000	Weak transcription	Fetal Heart	heart
31	chr3:28367200-28387800	Weak transcription	Fetal Brain Male	brain
32	chr3:28367200-28388800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:28367200-28389400	Weak transcription	Pancreas	Pancrea
34	chr3:28367400-28388800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:28368400-28377200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:28368400-28377200	Weak transcription	Left Ventricle	heart
37	chr3:28368400-28377400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:28368400-28377400	Weak transcription	HepG2	liver
39	chr3:28368400-28378600	Weak transcription	Psoas Muscle	Psoas
40	chr3:28368400-28378600	Weak transcription	NHEK	skin
41	chr3:28368400-28378800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:28368400-28387600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:28368400-28388800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:28369000-28381200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:28369000-28382000	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr3:28369000-28382400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr3:28369200-28378600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:28369600-28382200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:28370200-28378800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:28370200-28384000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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