Variant report

Variant	rs870070
Chromosome Location	chr3:195920278-195920279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:195793504..195812987-chr3:195901613..195938073,113	K562	blood:
2	chr3:195868030..195872313-chr3:195919244..195921988,5	MCF-7	breast:
3	chr3:195918010..195921527-chr3:195922088..195925554,4	K562	blood:
4	chr3:195796379..195810322-chr3:195910077..195926320,43	MCF-7	breast:
5	chr3:195793504..195812415-chr3:195915832..195927942,46	K562	blood:
6	chr3:195798458..195803942-chr3:195919017..195926093,8	MCF-7	breast:
7	chr3:195806798..195809921-chr3:195918894..195921572,5	MCF-7	breast:
8	chr3:195861753..195863466-chr3:195918246..195921048,2	K562	blood:
9	chr3:195869317..195872706-chr3:195916170..195921079,5	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC069257.9.1-8	chr3:195920236-195920505	l_2563_chr3:195910484-195920505_testes

No data

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

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs56699931	0.98[EUR][1000 genomes]
rs56850780	0.84[EUR][1000 genomes]
rs59412512	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60526982	0.95[EUR][1000 genomes]
rs6770218	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73210076	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73210077	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73210078	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73210081	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73210084	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73210095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73212105	0.98[EUR][1000 genomes]
rs73212119	0.93[EUR][1000 genomes]
rs73212122	0.96[EUR][1000 genomes]
rs73212124	0.96[EUR][1000 genomes]
rs73212127	0.98[EUR][1000 genomes]
rs73891224	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	esv32936	chr3:195916045-195940827	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs870070	PCYT1A	Cis_1M	lymphoblastoid	RTeQTL
rs870070	SLC51A	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195914200-195920600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:195914200-195921200	Weak transcription	Right Atrium	heart
3	chr3:195914200-195922200	Enhancers	Fetal Thymus	thymus
4	chr3:195914200-195923600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr3:195915600-195921800	Enhancers	Primary B cells from peripheral blood	blood
6	chr3:195915800-195921400	Enhancers	Primary B cells from cord blood	blood
7	chr3:195915800-195924400	Enhancers	Placenta	Placenta
8	chr3:195917400-195920600	Enhancers	K562	blood
9	chr3:195917400-195920800	Weak transcription	Ovary	ovary
10	chr3:195917800-195920600	Enhancers	Fetal Muscle Trunk	muscle
11	chr3:195917800-195921600	Enhancers	Fetal Muscle Leg	muscle
12	chr3:195918000-195921600	Enhancers	Primary hematopoietic stem cells	blood
13	chr3:195918000-195921800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:195918000-195922000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr3:195918200-195920600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:195918200-195920600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:195918200-195921600	Enhancers	Primary T cells fromperipheralblood	blood
18	chr3:195918200-195921800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:195918200-195922000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:195918200-195923600	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr3:195918400-195921200	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr3:195918800-195921400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr3:195918800-195922200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:195919000-195920400	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr3:195919000-195920400	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr3:195919000-195920600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:195919000-195920800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:195919000-195921600	Enhancers	Gastric	stomach
29	chr3:195919000-195921600	Enhancers	Pancreas	Pancrea
30	chr3:195919000-195922000	Enhancers	Fetal Heart	heart
31	chr3:195919000-195922000	Enhancers	Right Ventricle	heart
32	chr3:195919000-195922200	Enhancers	Fetal Intestine Small	intestine
33	chr3:195919000-195923600	Enhancers	Duodenum Mucosa	Duodenum
34	chr3:195919000-195923600	Enhancers	Stomach Mucosa	stomach
35	chr3:195919000-195923800	Enhancers	Fetal Intestine Large	intestine
36	chr3:195919200-195920400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:195919200-195920800	Enhancers	HSMM	muscle
38	chr3:195919200-195921000	Enhancers	Brain Germinal Matrix	brain
39	chr3:195919200-195921400	Enhancers	Brain Anterior Caudate	brain
40	chr3:195919400-195921200	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr3:195919400-195929400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:195919600-195920400	Enhancers	Hela-S3	cervix
43	chr3:195919600-195920600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:195919600-195920800	Enhancers	Brain Substantia Nigra	brain
45	chr3:195919600-195921000	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr3:195919600-195921600	Enhancers	Liver	Liver
47	chr3:195919600-195922800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr3:195919800-195920600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:195919800-195920600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:195919800-195920600	Weak transcription	Adipose Nuclei	Adipose

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