Variant report

Variant	rs12649430
Chromosome Location	chr4:175512653-175512654
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10866372	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11133047	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11133048	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133049	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11722219	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11725394	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11728575	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733443	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11932191	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12647899	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12649779	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12650961	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103368	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13130070	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13130669	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1820525	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2555652	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34618616	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4695934	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[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	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv881376	chr4:175466101-175513812	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1018390	chr4:175475505-175969742	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv880800	chr4:175476462-175513812	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv881268	chr4:175476462-175513812	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv881481	chr4:175476462-175515345	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv881192	chr4:175476462-175523073	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv880379	chr4:175479889-175513812	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv881565	chr4:175479889-175515345	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv881297	chr4:175479889-175515940	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv880684	chr4:175479889-175523073	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv880403	chr4:175485318-175535392	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv880679	chr4:175502088-175552622	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv880584	chr4:175505749-175644689	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12649430	HPGD	cis	Whole Blood	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175502400-175513400	Weak transcription	NHDF-Ad	bronchial
2	chr4:175510600-175513200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:175511000-175512800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr4:175511200-175512800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr4:175511600-175515600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr4:175512000-175515600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr4:175512000-175516200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:175512200-175512800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:175512200-175513800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr4:175512200-175514800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:175512400-175512800	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr4:175512400-175512800	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr4:175512400-175513000	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr4:175512400-175513000	Enhancers	Stomach Mucosa	stomach
15	chr4:175512400-175514200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:175512600-175512800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:175512600-175513000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr4:175512600-175513400	Enhancers	Primary B cells from peripheral blood	blood
19	chr4:175512600-175513400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:175512600-175514200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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