Variant report

Variant	rs3844291
Chromosome Location	chr3:52341215-52341216
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52330648..52332485-chr3:52338517..52342537,3	K562	blood:
2	chr3:52330648..52333438-chr3:52339681..52342537,3	K562	blood:
3	chr3:52335740..52338441-chr3:52339077..52343007,7	K562	blood:
4	chr3:52340180..52343707-chr3:52344223..52347633,5	K562	blood:

Variant related genes	Relation type
ENSG00000242797	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1060330	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs11712164	0.83[JPT][hapmap]
rs11717383	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs13094687	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs1546737	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2267847	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2272088	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2276834	0.85[ASN][1000 genomes]
rs34228726	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34569561	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs353547	0.81[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs3852063	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3852064	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3890123	1.00[YRI][hapmap]
rs57615517	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57630131	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59565798	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs610060	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6445358	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs6766038	0.83[YRI][hapmap]
rs730050	0.90[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs731831	0.90[CEU][hapmap]
rs7614727	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7618915	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7622851	0.91[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs7629072	0.83[ASN][1000 genomes]
rs9311474	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
4	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
5	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
6	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
7	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
8	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3844291	FLJ12442	cis	multi-tissue	Pritchard
rs3844291	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52327200-52351600	Weak transcription	Aorta	Aorta
2	chr3:52327400-52351600	Weak transcription	Brain Anterior Caudate	brain
3	chr3:52327600-52344600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:52328000-52347000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:52328200-52366000	Weak transcription	Brain Angular Gyrus	brain
6	chr3:52328800-52367600	Weak transcription	Brain Substantia Nigra	brain
7	chr3:52329200-52351600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:52330200-52343400	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:52330200-52343400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:52330200-52345400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:52330400-52378600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:52331000-52343200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:52331200-52342800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:52333000-52351600	Weak transcription	Thymus	Thymus
15	chr3:52334000-52351400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:52334200-52347400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:52334200-52349600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:52334400-52344000	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:52334400-52347200	Weak transcription	Esophagus	oesophagus
20	chr3:52334600-52341400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:52334600-52342200	Weak transcription	Liver	Liver
22	chr3:52334600-52348000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:52335000-52347600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:52335200-52343200	Weak transcription	Placenta	Placenta
25	chr3:52335200-52343600	Weak transcription	Lung	lung
26	chr3:52335200-52345000	Weak transcription	HSMMtube	muscle
27	chr3:52335200-52347200	Weak transcription	Left Ventricle	heart
28	chr3:52335200-52347400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:52335200-52347600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:52335400-52344000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:52335400-52345000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:52335400-52351400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr3:52336800-52343200	Genic enhancers	Fetal Intestine Small	intestine
34	chr3:52337200-52345000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:52337400-52347200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:52338200-52342200	Enhancers	Fetal Intestine Large	intestine
37	chr3:52338400-52351400	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:52338600-52342800	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr3:52338600-52344000	Weak transcription	Primary B cells from cord blood	blood
40	chr3:52338800-52342600	Enhancers	Duodenum Mucosa	Duodenum
41	chr3:52339200-52341400	Enhancers	Colonic Mucosa	Colon
42	chr3:52339200-52342600	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr3:52339400-52341400	Enhancers	HepG2	liver
44	chr3:52339400-52342200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:52339400-52347400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:52339600-52341400	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:52339800-52351200	Weak transcription	Right Ventricle	heart
48	chr3:52340000-52342400	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr3:52340200-52342200	Weak transcription	Adipose Nuclei	Adipose
50	chr3:52340200-52342200	Weak transcription	Gastric	stomach

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