Variant report

Variant	rs59815219
Chromosome Location	chr3:195996188-195996189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:195995012..195996670-chr3:196038187..196039923,2	MCF-7	breast:
2	chr3:195994801..195996636-chr3:196013767..196015468,2	K562	blood:
3	chr3:195989073..195991796-chr3:195994063..195996834,4	K562	blood:
4	chr3:195987889..195991350-chr3:195994108..195996834,3	K562	blood:
5	chr3:195995964..195998630-chr3:196022828..196024576,2	K562	blood:

Variant related genes	Relation type
ENSG00000213123	Chromatin interaction
ENSG00000161217	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11185520	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12630070	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60680644	0.90[ASN][1000 genomes]
rs67723323	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73212143	0.87[ASN][1000 genomes]
rs7636149	0.81[AFR][1000 genomes]
rs7639752	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs939883	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs59815219	PCYT1A	Cis_1M	lymphoblastoid	RTeQTL
rs59815219	SLC51A	cis	Heart Left Ventricle	GTEx
rs59815219	SLC51A	cis	Adipose Subcutaneous	GTEx
rs59815219	SLC51A	cis	Esophagus Muscularis	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195965800-196012400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:195969600-196012400	Weak transcription	Fetal Brain Male	brain
3	chr3:195973400-195997200	Weak transcription	Small Intestine	intestine
4	chr3:195974400-195999800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:195974600-195999800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:195974800-195999600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:195974800-195999600	Weak transcription	Pancreas	Pancrea
8	chr3:195974800-196005000	Weak transcription	Stomach Mucosa	stomach
9	chr3:195975000-195997200	Weak transcription	Esophagus	oesophagus
10	chr3:195975000-195999600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:195981400-195997800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:195982400-195997600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:195983200-195999800	Weak transcription	Psoas Muscle	Psoas
14	chr3:195984000-195997400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:195984800-196005000	Weak transcription	Fetal Heart	heart
16	chr3:195987400-195998200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:195987600-195997800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:195988000-195999600	Weak transcription	HSMMtube	muscle
19	chr3:195989600-195996600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:195989800-195997800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:195989800-195998000	Strong transcription	Duodenum Mucosa	Duodenum
22	chr3:195989800-195998000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:195990000-195997800	Strong transcription	Fetal Stomach	stomach
24	chr3:195990200-195997600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr3:195990200-195997800	Strong transcription	Fetal Intestine Large	intestine
26	chr3:195990200-195997800	Strong transcription	Fetal Muscle Trunk	muscle
27	chr3:195990200-195998200	Strong transcription	Fetal Intestine Small	intestine
28	chr3:195990400-195999800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr3:195990400-196000000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:195990400-196006400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:195990800-195996200	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:195990800-195997200	Strong transcription	Fetal Thymus	thymus
33	chr3:195990800-195997600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr3:195990800-195998000	Strong transcription	Primary T cells from cord blood	blood
35	chr3:195991400-195997400	Strong transcription	HSMM	muscle
36	chr3:195991400-195997800	Strong transcription	Fetal Muscle Leg	muscle
37	chr3:195991400-195998000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:195991800-196012400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:195992200-195996600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:195992400-195997800	Strong transcription	Lung	lung
41	chr3:195992400-195997800	Strong transcription	HepG2	liver
42	chr3:195992800-195996600	Strong transcription	Brain Anterior Caudate	brain
43	chr3:195993000-195996800	Strong transcription	Fetal Brain Female	brain
44	chr3:195993000-196005200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr3:195993400-195996400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr3:195993400-195996600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr3:195993400-195997400	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:195993400-195997600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:195993400-195997600	Strong transcription	Placenta	Placenta
50	chr3:195993400-195998200	Strong transcription	Ovary	ovary

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