Variant report

Variant	rs9850946
Chromosome Location	chr3:196198209-196198210
allele	A/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	chr3:196198167-196199642	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:196192779..196196308-chr3:196197005..196200589,3	K562	blood:
2	chr3:196194808..196197230-chr3:196197915..196199968,2	K562	blood:
3	chr3:196197868..196200797-chr3:196203999..196206906,2	K562	blood:

Variant related genes	Relation type
ENSG00000273013	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10470712	1.00[YRI][hapmap]
rs13324746	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs28463746	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv878185	chr3:196158773-196199204	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv878186	chr3:196158773-196219794	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9850946	HDGFRP3	trans	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196171000-196198400	Weak transcription	Fetal Brain Female	brain
2	chr3:196171400-196198600	Weak transcription	Ovary	ovary
3	chr3:196173000-196198600	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:196175200-196198400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:196177000-196198400	Weak transcription	Pancreas	Pancrea
6	chr3:196177800-196198600	Weak transcription	Small Intestine	intestine
7	chr3:196178200-196198400	Weak transcription	Brain Germinal Matrix	brain
8	chr3:196178200-196198600	Weak transcription	Psoas Muscle	Psoas
9	chr3:196180600-196198400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:196182200-196213600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:196182600-196198400	Weak transcription	Left Ventricle	heart
12	chr3:196183000-196198400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:196185200-196198600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:196187600-196198400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:196189200-196198400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:196189200-196198400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:196189600-196198400	Weak transcription	Spleen	Spleen
18	chr3:196190600-196198400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:196191000-196198400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:196191200-196198400	Weak transcription	Fetal Intestine Large	intestine
21	chr3:196191800-196216800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:196192600-196198400	Weak transcription	HSMMtube	muscle
23	chr3:196193200-196198600	Weak transcription	HMEC	breast
24	chr3:196193400-196198400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:196193400-196198800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:196193400-196200200	Weak transcription	Fetal Kidney	kidney
27	chr3:196193400-196209400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr3:196193600-196214600	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr3:196194000-196198400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:196194200-196198400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:196194200-196198400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:196194200-196202200	Strong transcription	HUVEC	blood vessel
33	chr3:196194200-196215000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:196194200-196217400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr3:196194400-196198400	Weak transcription	NHLF	lung
36	chr3:196194400-196211200	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:196194400-196216600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:196194600-196198400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:196194600-196214600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:196194600-196214800	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:196194600-196215800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:196194800-196215000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:196195000-196198400	Weak transcription	HepG2	liver
44	chr3:196195000-196198400	Weak transcription	HSMM	muscle
45	chr3:196195000-196214800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:196195200-196202400	Strong transcription	Hela-S3	cervix
47	chr3:196195200-196215200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:196195400-196214800	Strong transcription	Liver	Liver
49	chr3:196195400-196215600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr3:196195600-196202400	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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