Variant report

Variant	rs2167417
Chromosome Location	chr19:52203458-52203459
allele	G/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	chr19:52199636-52204065	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52196159..52199511-chr19:52202868..52206043,4	K562	blood:
2	chr19:52193714..52195914-chr19:52201685..52203516,2	K562	blood:
3	chr19:52202858..52204622-chr19:52205680..52207387,2	K562	blood:

Variant related genes	Relation type
SPACA6P	TF binding region
ENSG00000269959	Chromatin interaction
ENSG00000182310	Chromatin interaction
ENSG00000273318	Chromatin interaction
ENSG00000207550	Chromatin interaction
ENSG00000208008	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11881781	0.97[ASN][1000 genomes]
rs2167418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864920	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864922	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34764077	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35653323	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802841	1.00[ASN][1000 genomes]
rs7252496	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73054871	0.97[ASN][1000 genomes]
rs8107937	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
2	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
3	nsv482909	chr19:52091735-52266700	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	533 gene(s)	inside rSNPs	diseases
4	nsv1064914	chr19:52103914-52231564	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	529 gene(s)	inside rSNPs	diseases
5	nsv544052	chr19:52103914-52271247	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	531 gene(s)	inside rSNPs	diseases
6	nsv1056825	chr19:52103914-52359815	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
7	nsv544053	chr19:52103914-52359815	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
8	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
9	esv1843680	chr19:52131510-52211749	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
10	nsv1066046	chr19:52147399-52271247	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
11	nsv544054	chr19:52147399-52271247	Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
12	nsv912296	chr19:52182363-52231032	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	518 gene(s)	inside rSNPs	diseases
13	nsv915725	chr19:52184488-52439676	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
14	nsv9742	chr19:52187538-52221742	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	517 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2167417	HAS1	cis	Whole Blood	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52194200-52205400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:52194600-52205800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr19:52194600-52207000	Weak transcription	Psoas Muscle	Psoas
4	chr19:52194800-52204600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr19:52194800-52205200	Weak transcription	Stomach Mucosa	stomach
6	chr19:52195000-52205600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:52195000-52205600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr19:52195000-52205800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr19:52195000-52205800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:52195200-52205800	Weak transcription	Primary T cells from cord blood	blood
11	chr19:52195400-52204600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr19:52195400-52207200	Weak transcription	Hela-S3	cervix
13	chr19:52195600-52204600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr19:52195600-52204800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr19:52195800-52204600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr19:52196200-52204800	Weak transcription	Colonic Mucosa	Colon
17	chr19:52196200-52204800	Strong transcription	NHEK	skin
18	chr19:52196200-52205600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:52196200-52205600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:52196400-52204600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr19:52196400-52204600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:52196400-52205200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr19:52196400-52206400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:52196400-52206600	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr19:52196600-52204600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr19:52196600-52205200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:52196600-52205200	Strong transcription	Adipose Nuclei	Adipose
28	chr19:52196600-52205800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr19:52196800-52205000	Strong transcription	Brain Germinal Matrix	brain
30	chr19:52196800-52205400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:52197000-52204600	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr19:52197000-52204800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:52197000-52204800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:52197000-52205200	Strong transcription	Fetal Muscle Trunk	muscle
35	chr19:52197000-52205600	Strong transcription	Fetal Lung	lung
36	chr19:52197000-52205800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:52197200-52204400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr19:52197200-52204800	Strong transcription	HMEC	breast
39	chr19:52197600-52205400	Strong transcription	Fetal Stomach	stomach
40	chr19:52197800-52203600	Strong transcription	Lung	lung
41	chr19:52197800-52205200	Strong transcription	Fetal Muscle Leg	muscle
42	chr19:52198000-52203800	Strong transcription	Ovary	ovary
43	chr19:52198200-52204400	Strong transcription	Placenta	Placenta
44	chr19:52198200-52205200	Weak transcription	Esophagus	oesophagus
45	chr19:52198200-52205400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr19:52198600-52204400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr19:52198600-52204400	Weak transcription	Fetal Heart	heart
48	chr19:52198600-52204600	Strong transcription	Left Ventricle	heart
49	chr19:52198600-52204800	Strong transcription	A549	lung
50	chr19:52198600-52205200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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