Variant report

Variant	rs56875789
Chromosome Location	chr3:195958882-195958883
allele	C/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	chr3:195957762-195959451	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:195958699-195960775	K562	blood:	n/a	n/a
3	POLR2A	chr3:195958562-195959074	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:195957646-195959559	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:195952367..195954245-chr3:195957237..195960071,2	K562	blood:

Variant related genes	Relation type
SLC51A	TF binding region
ENSG00000163959	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11185519	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12632779	0.81[ASN][1000 genomes]
rs12634587	0.81[ASN][1000 genomes]
rs12635925	0.81[ASN][1000 genomes]
rs1875088	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2342309	0.98[ASN][1000 genomes]
rs3772107	0.81[ASN][1000 genomes]
rs56701784	0.81[ASN][1000 genomes]
rs56867360	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57987393	0.82[ASN][1000 genomes]
rs58845625	0.81[ASN][1000 genomes]
rs60276076	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61608982	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67044678	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67261052	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72611184	0.98[ASN][1000 genomes]
rs72611185	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72611186	0.98[ASN][1000 genomes]
rs72611187	0.81[ASN][1000 genomes]
rs72611190	0.81[ASN][1000 genomes]
rs7429803	0.98[ASN][1000 genomes]
rs7617236	0.81[ASN][1000 genomes]
rs7635355	0.81[ASN][1000 genomes]
rs7637009	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7638797	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7641135	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs870339	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs939885	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	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
5	nsv878171	chr3:195677895-195959924	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv1008512	chr3:195709662-195974936	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
8	nsv1009105	chr3:195769609-195984388	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
10	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
11	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
13	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
14	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
15	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
16	nsv878175	chr3:195907653-195973244	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	nsv1014159	chr3:195908999-195968512	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
18	nsv878176	chr3:195926234-195959924	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv878178	chr3:195929268-195998451	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
20	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
21	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
22	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS 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	33 gene(s)	inside rSNPs	diseases
23	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56875789	PCYT1A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195944200-195964000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:195945000-195968400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:195946600-195965600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:195946800-195962600	Weak transcription	Primary T cells from cord blood	blood
5	chr3:195946800-195964200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:195946800-195967400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:195947000-195959000	Weak transcription	Dnd41	blood
8	chr3:195947000-195960800	Weak transcription	Fetal Intestine Large	intestine
9	chr3:195947000-195963800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:195947000-195964000	Weak transcription	Colonic Mucosa	Colon
11	chr3:195947200-195962000	Weak transcription	Fetal Brain Male	brain
12	chr3:195947200-195962600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:195947200-195962600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:195948000-195970400	Strong transcription	Liver	Liver
15	chr3:195950400-195959800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:195950400-195964400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:195952600-195963200	Weak transcription	K562	blood
18	chr3:195953200-195963800	Weak transcription	Brain Germinal Matrix	brain
19	chr3:195954600-195960000	Weak transcription	Fetal Brain Female	brain
20	chr3:195954600-195960400	Weak transcription	Lung	lung
21	chr3:195954600-195962200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:195954600-195963800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:195954600-195964600	Weak transcription	Brain Angular Gyrus	brain
24	chr3:195954600-195964800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:195954800-195962800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:195954800-195963800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:195954800-195963800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:195954800-195963800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:195954800-195964600	Weak transcription	NHDF-Ad	bronchial
30	chr3:195954800-195968600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:195955000-195963000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:195955000-195963200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:195955000-195963800	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:195955000-195963800	Weak transcription	HMEC	breast
35	chr3:195955000-195964000	Weak transcription	Fetal Lung	lung
36	chr3:195955200-195959600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:195955200-195961000	Weak transcription	Fetal Muscle Leg	muscle
38	chr3:195955200-195963000	Weak transcription	Spleen	Spleen
39	chr3:195955200-195963200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr3:195955200-195964200	Weak transcription	HSMM	muscle
41	chr3:195955400-195963600	Weak transcription	Gastric	stomach
42	chr3:195955400-195964000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr3:195955400-195968400	Weak transcription	Pancreas	Pancrea
44	chr3:195955600-195959400	Weak transcription	HepG2	liver
45	chr3:195955600-195959800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:195955600-195962200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:195955600-195963000	Weak transcription	Left Ventricle	heart
48	chr3:195955600-195963600	Weak transcription	Right Ventricle	heart
49	chr3:195955600-195964200	Weak transcription	HSMMtube	muscle
50	chr3:195955800-195959800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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