Variant report

Variant	rs2167418
Chromosome Location	chr19:52204942-52204943
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	chr19:52204903-52210059	K562	blood:	n/a	n/a
2	POLR2A	chr19:52204938-52205374	K562	blood:	n/a	n/a
3	RCOR1	chr19:52204845-52205366	K562	blood:	n/a	n/a
4	NR3C1	chr19:52204648-52205015	A549	lung:	n/a	n/a
5	POLR2A	chr19:52204570-52209007	K562	blood:	n/a	n/a
6	JUND	chr19:52204803-52205947	K562	blood:	n/a	n/a
7	MAZ	chr19:52204752-52207931	K562	blood:	n/a	chr19:52206354-52206364 chr19:52205773-52205783
8	NR2F2	chr19:52204830-52206006	K562	blood:	n/a	n/a
9	MYC	chr19:52204843-52205951	K562	blood:	n/a	chr19:52205773-52205783
10	POLR2A	chr19:52204692-52204992	MCF-7	breast:	n/a	n/a
11	ZMIZ1	chr19:52204873-52204981	K562	blood:	n/a	n/a
12	MAFK	chr19:52204774-52204970	K562	blood:	n/a	n/a
13	POLR2A	chr19:52204333-52208183	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr19:52204780-52207896	K562	blood:	n/a	n/a
15	NR3C1	chr19:52204638-52205069	A549	lung:	n/a	n/a
16	TBL1XR1	chr19:52204870-52205379	K562	blood:	n/a	n/a
17	BHLHE40	chr19:52204711-52206043	K562	blood:	n/a	n/a
18	POLR2A	chr19:52204529-52208440	K562	blood:	n/a	n/a
19	IRF1	chr19:52204773-52207739	K562	blood:	n/a	chr19:52206596-52206610 chr19:52207440-52207454 chr19:52207480-52207494 chr19:52207194-52207208 chr19:52205431-52205445 chr19:52205768-52205782 chr19:52206149-52206163 chr19:52205497-52205511 chr19:52206355-52206369 chr19:52205565-52205579 chr19:52207213-52207227 chr19:52205738-52205752
20	CCNT2	chr19:52204702-52205894	K562	blood:	n/a	chr19:52205772-52205781 chr19:52205710-52205719 chr19:52205435-52205444 chr19:52205742-52205751
21	POLR2A	chr19:52204545-52209003	A549	lung:	n/a	n/a
22	POLR2A	chr19:52204340-52205047	U87	brain:	n/a	n/a
23	POLR2A	chr19:52204703-52208998	K562	blood:	n/a	n/a
24	MYC	chr19:52204856-52205851	K562	blood:	n/a	chr19:52205773-52205783
25	CBX3	chr19:52204549-52204959	K562	blood:	n/a	n/a
26	POLR2A	chr19:52204318-52214138	PFSK-1	brain:	n/a	n/a
27	MAX	chr19:52204738-52207859	K562	blood:	n/a	chr19:52206354-52206364 chr19:52205773-52205783
28	RCOR1	chr19:52204725-52206054	K562	blood:	n/a	n/a
29	UBTF	chr19:52204800-52206049	K562	blood:	n/a	n/a
30	TEAD4	chr19:52204915-52206056	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52204118..52207726-chr19:52271324..52274498,3	K562	blood:
2	chr19:52196159..52199511-chr19:52202868..52206043,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FPR2-1	chr19:52204911-52205023	ENSG00000182310.8

Variant related genes	Relation type
SPACA6P	TF binding region
ENSG00000182310	Chromatin interaction
ENSG00000171049	Chromatin interaction
ENSG00000273318	Chromatin interaction
ENSG00000208008	Chromatin interaction
ENSG00000269959	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11881781	0.97[ASN][1000 genomes]
rs2167417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864920	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34764077	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35653323	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802841	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs7252496	0.90[AMR][1000 genomes];0.85[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2167418	HAS1	cis	Whole Blood	GTEx
rs2167418	ZNF264	cis	parietal	SCAN
rs2167418	ZNF702P	cis	parietal	SCAN
rs2167418	ZNF587	cis	cerebellum	SCAN
rs2167418	ZNF304	cis	parietal	SCAN
rs2167418	ZNF784	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

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	chr19:52194800-52205200	Weak transcription	Stomach Mucosa	stomach
5	chr19:52195000-52205600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:52195000-52205600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr19:52195000-52205800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr19:52195000-52205800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:52195200-52205800	Weak transcription	Primary T cells from cord blood	blood
10	chr19:52195400-52207200	Weak transcription	Hela-S3	cervix
11	chr19:52196200-52205600	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr19:52196200-52205600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr19:52196400-52205200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:52196400-52206400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:52196400-52206600	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr19:52196600-52205200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:52196600-52205200	Strong transcription	Adipose Nuclei	Adipose
18	chr19:52196600-52205800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr19:52196800-52205000	Strong transcription	Brain Germinal Matrix	brain
20	chr19:52196800-52205400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:52197000-52205200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr19:52197000-52205600	Strong transcription	Fetal Lung	lung
23	chr19:52197000-52205800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:52197600-52205400	Strong transcription	Fetal Stomach	stomach
25	chr19:52197800-52205200	Strong transcription	Fetal Muscle Leg	muscle
26	chr19:52198200-52205200	Weak transcription	Esophagus	oesophagus
27	chr19:52198200-52205400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr19:52198600-52205200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:52198600-52205400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:52198600-52205400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr19:52198800-52205200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr19:52198800-52205200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:52198800-52205400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:52198800-52205400	Strong transcription	Fetal Brain Female	brain
35	chr19:52199000-52205200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr19:52200200-52206000	Strong transcription	HUVEC	blood vessel
37	chr19:52200400-52205600	Weak transcription	Colon Smooth Muscle	Colon
38	chr19:52201800-52205400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:52202000-52205400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:52202000-52205800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr19:52202000-52206800	Strong transcription	Osteobl	bone
42	chr19:52202200-52205400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:52202200-52205400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:52202200-52205800	Weak transcription	Brain Substantia Nigra	brain
45	chr19:52202400-52205200	Weak transcription	Spleen	Spleen
46	chr19:52202400-52205800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:52202400-52206000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:52202400-52207200	Weak transcription	Aorta	Aorta
49	chr19:52202600-52205800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr19:52202600-52206800	Weak transcription	Fetal Brain Male	brain

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