Variant report

Variant	rs6770218
Chromosome Location	chr3:195914403-195914404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:195801020..195810289-chr3:195902611..195915225,28	K562	blood:
2	chr3:195793504..195812987-chr3:195901613..195938073,113	K562	blood:
3	chr3:195869232..195870927-chr3:195912460..195915353,2	MCF-7	breast:
4	chr3:195796379..195810322-chr3:195910077..195926320,43	MCF-7	breast:
5	chr3:195800491..195804775-chr3:195913481..195918135,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000072274	Chromatin interaction
ENSG00000224652	Chromatin interaction
ENSG00000252174	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12489737	0.89[ASN][1000 genomes]
rs56699931	0.93[EUR][1000 genomes]
rs59412512	0.91[EUR][1000 genomes]
rs60526982	0.90[EUR][1000 genomes]
rs73210076	0.91[EUR][1000 genomes]
rs73210077	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73210078	0.91[EUR][1000 genomes]
rs73210081	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73210084	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73210095	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73212105	0.93[EUR][1000 genomes]
rs73212119	0.88[EUR][1000 genomes]
rs73212122	0.91[EUR][1000 genomes]
rs73212124	0.91[EUR][1000 genomes]
rs73212127	0.93[EUR][1000 genomes]
rs73891224	0.91[EUR][1000 genomes]
rs870070	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 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	nsv532214	chr3:195762648-195916068	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
9	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
10	nsv1005558	chr3:195789462-195919077	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
11	nsv536890	chr3:195789462-195919077	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv998042	chr3:195840858-195934070	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	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
14	nsv593070	chr3:195854279-195924203	Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv878174	chr3:195858887-195949541	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
16	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
17	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
18	nsv1004194	chr3:195864466-195919077	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	nsv536891	chr3:195864466-195919077	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	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
21	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
22	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
23	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
24	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
25	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6770218	PCYT1A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195907200-195919000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:195910800-195915600	Weak transcription	Hela-S3	cervix
3	chr3:195910800-195915800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:195910800-195916000	Weak transcription	Fetal Intestine Small	intestine
5	chr3:195910800-195919200	Weak transcription	HSMM	muscle
6	chr3:195911400-195916000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:195912000-195914800	Enhancers	Fetal Muscle Leg	muscle
8	chr3:195912600-195915000	Enhancers	Primary hematopoietic stem cells	blood
9	chr3:195913000-195914800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr3:195913200-195914800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr3:195913400-195914800	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr3:195913400-195915000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:195913600-195914800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:195913800-195919000	Weak transcription	Gastric	stomach
15	chr3:195913800-195919200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr3:195913800-195920000	Weak transcription	Lung	lung
17	chr3:195914000-195915800	Weak transcription	Placenta	Placenta
18	chr3:195914000-195918200	Weak transcription	Psoas Muscle	Psoas
19	chr3:195914000-195918800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:195914000-195919000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr3:195914000-195919000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:195914000-195919200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:195914200-195914600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:195914200-195914600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr3:195914200-195915000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:195914200-195915200	Enhancers	Primary B cells from peripheral blood	blood
27	chr3:195914200-195915800	Weak transcription	HepG2	liver
28	chr3:195914200-195916000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:195914200-195916400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:195914200-195916400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:195914200-195916400	Weak transcription	Stomach Mucosa	stomach
32	chr3:195914200-195918400	Weak transcription	Colonic Mucosa	Colon
33	chr3:195914200-195918800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:195914200-195918800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:195914200-195919000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr3:195914200-195919000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:195914200-195919000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:195914200-195919000	Weak transcription	Adipose Nuclei	Adipose
39	chr3:195914200-195919000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:195914200-195919000	Weak transcription	Esophagus	oesophagus
41	chr3:195914200-195919000	Weak transcription	Left Ventricle	heart
42	chr3:195914200-195919000	Weak transcription	Right Ventricle	heart
43	chr3:195914200-195919200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:195914200-195919200	Weak transcription	Brain Anterior Caudate	brain
45	chr3:195914200-195919200	Weak transcription	HSMMtube	muscle
46	chr3:195914200-195919400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:195914200-195919400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:195914200-195919400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:195914200-195919400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:195914200-195920000	Weak transcription	Fetal Lung	lung

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