Variant report

Variant	rs13324746
Chromosome Location	chr3:196226245-196226246
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196221498..196224147-chr3:196224892..196227326,3	K562	blood:
2	chr3:196209119..196211761-chr3:196224016..196226759,2	K562	blood:
3	chr3:195954091..195957267-chr3:196224695..196228323,3	K562	blood:
4	chr3:196225951..196229671-chr3:196232919..196236791,4	K562	blood:

Variant related genes	Relation type
ENSG00000163959	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10470712	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10470716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13324149	1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[AMR][1000 genomes]
rs28395177	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35405598	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35864132	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9850946	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs9877313	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv469831	chr3:196071603-196235225	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv482542	chr3:196071603-196235225	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
9	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13324746	HDGFRP3	trans	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196199400-196227000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:196213000-196226800	Weak transcription	Fetal Kidney	kidney
3	chr3:196213800-196226600	Weak transcription	Brain Substantia Nigra	brain
4	chr3:196214400-196226400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:196214400-196226600	Weak transcription	Aorta	Aorta
6	chr3:196214400-196226800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:196214400-196226800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:196214400-196226800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:196214400-196226800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:196214400-196226800	Weak transcription	Brain Anterior Caudate	brain
11	chr3:196214400-196226800	Weak transcription	Pancreas	Pancrea
12	chr3:196214400-196227000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:196214400-196227000	Weak transcription	Fetal Lung	lung
14	chr3:196214400-196227000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:196214400-196228200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:196214600-196226400	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:196214600-196226400	Weak transcription	Spleen	Spleen
18	chr3:196214600-196226800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:196214600-196226800	Weak transcription	Colonic Mucosa	Colon
20	chr3:196214600-196226800	Weak transcription	Fetal Intestine Large	intestine
21	chr3:196214600-196226800	Weak transcription	Lung	lung
22	chr3:196214800-196227200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:196215000-196227000	Weak transcription	Placenta	Placenta
24	chr3:196215800-196226800	Weak transcription	Right Atrium	heart
25	chr3:196217600-196226800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:196217800-196226800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:196217800-196227000	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:196218000-196227000	Weak transcription	Brain Angular Gyrus	brain
29	chr3:196221200-196226600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr3:196222800-196226400	Weak transcription	Liver	Liver
31	chr3:196223400-196226800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:196223400-196226800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:196223400-196226800	Weak transcription	NHLF	lung
34	chr3:196223400-196227000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:196223600-196226400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:196223600-196226800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr3:196223800-196226600	Weak transcription	Primary T cells from cord blood	blood
38	chr3:196223800-196226600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:196223800-196226600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:196223800-196226800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr3:196223800-196226800	Weak transcription	Primary B cells from cord blood	blood
42	chr3:196223800-196226800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:196223800-196226800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:196223800-196227000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr3:196224600-196226600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:196224600-196226800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:196224600-196226800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr3:196224600-196226800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:196224800-196226600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr3:196224800-196227400	Transcr. at gene 5' and 3'	Dnd41	blood

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