Variant report

Variant	rs561804285
Chromosome Location	chr3:42639281-42639282
allele	A/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	POLR2A	chr3:42636237-42639709	K562	blood:	n/a	n/a
2	POLR2A	chr3:42639075-42639701	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:42639079-42639372	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42629943..42634676-chr3:42635408..42643782,10	MCF-7	breast:
2	chr3:42631664..42634178-chr3:42636385..42639345,6	MCF-7	breast:
3	chr3:42619900..42621497-chr3:42638395..42640003,2	MCF-7	breast:
4	chr3:42632553..42639930-chr3:42692933..42696882,8	K562	blood:

Variant related genes	Relation type
NKTR	TF binding region
ENSG00000008324	Chromatin interaction
ENSG00000114853	Chromatin interaction
ENSG00000230084	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

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	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3415147	chr3:42638848-42641746	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	esv3404290	chr3:42638948-42643146	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42633200-42641400	Weak transcription	Aorta	Aorta
2	chr3:42633200-42641600	Weak transcription	Gastric	stomach
3	chr3:42633400-42641200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr3:42633400-42641200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:42633400-42641200	Weak transcription	HSMMtube	muscle
6	chr3:42633400-42641400	Weak transcription	Ovary	ovary
7	chr3:42633400-42641400	Weak transcription	Psoas Muscle	Psoas
8	chr3:42633400-42641400	Weak transcription	Right Ventricle	heart
9	chr3:42633400-42641600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:42633400-42641600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:42633400-42641600	Weak transcription	Esophagus	oesophagus
12	chr3:42633400-42641600	Weak transcription	Spleen	Spleen
13	chr3:42633600-42639400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:42633600-42641200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:42633600-42641200	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:42633600-42641200	Weak transcription	Fetal Kidney	kidney
17	chr3:42633600-42641200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:42633600-42641200	Weak transcription	Right Atrium	heart
19	chr3:42633600-42641200	Weak transcription	NHEK	skin
20	chr3:42633600-42641400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:42633600-42641400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:42633600-42641400	Weak transcription	Brain Anterior Caudate	brain
23	chr3:42633600-42641600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:42633600-42641600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:42633600-42641600	Weak transcription	Pancreas	Pancrea
26	chr3:42633800-42641200	Weak transcription	Brain Germinal Matrix	brain
27	chr3:42634000-42641200	Weak transcription	Fetal Intestine Small	intestine
28	chr3:42634000-42641600	Weak transcription	Lung	lung
29	chr3:42634400-42641200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:42634600-42641200	Weak transcription	Fetal Brain Male	brain
31	chr3:42635000-42639400	Strong transcription	HSMM	muscle
32	chr3:42635000-42639600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:42635400-42641200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:42635400-42641200	Weak transcription	Brain Angular Gyrus	brain
35	chr3:42635600-42640800	Weak transcription	Hela-S3	cervix
36	chr3:42635600-42641200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:42635600-42641200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:42635600-42641200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:42635600-42641200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:42635600-42641200	Weak transcription	Fetal Stomach	stomach
41	chr3:42635600-42641200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:42635600-42641400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:42635600-42641600	Weak transcription	Small Intestine	intestine
44	chr3:42635800-42641200	Weak transcription	HepG2	liver
45	chr3:42636000-42641200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr3:42636000-42641200	Weak transcription	Brain Hippocampus Middle	brain
47	chr3:42636000-42641200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:42636000-42641400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:42636200-42641200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr3:42636200-42641200	Weak transcription	A549	lung

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