Variant report

Variant	rs7130
Chromosome Location	chr3:45959515-45959516
allele	A/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	chr3:45957672-45959751	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45958439..45960531-chr3:46002605..46005170,2	K562	blood:

Variant related genes	Relation type
LZTFL1	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1047444	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1488373	0.95[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1488374	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1532070	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2191030	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs2373088	0.81[EUR][1000 genomes]
rs6441934	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6764244	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6806802	0.82[EUR][1000 genomes]
rs7618618	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7634640	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7652331	1.00[YRI][hapmap]
rs9311379	0.84[EUR][1000 genomes]
rs9810934	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7130	FYCO1	cis	Nerve Tibial	GTEx
rs7130	FYCO1	cis	lung	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45932400-45960200	Weak transcription	Fetal Intestine Small	intestine
2	chr3:45934000-45960200	Weak transcription	Right Ventricle	heart
3	chr3:45940000-45959800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:45941400-45960000	Weak transcription	Adipose Nuclei	Adipose
5	chr3:45943000-45961000	Weak transcription	Brain Substantia Nigra	brain
6	chr3:45943600-45961200	Weak transcription	Gastric	stomach
7	chr3:45946200-45960400	Weak transcription	Aorta	Aorta
8	chr3:45947000-45960200	Weak transcription	Lung	lung
9	chr3:45948200-45961000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:45948400-45961600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:45948800-45960200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:45949200-45962400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:45949800-45962600	Weak transcription	HepG2	liver
14	chr3:45950000-45960800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:45950200-45959800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:45950200-45960000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:45950200-45960400	Weak transcription	Pancreas	Pancrea
18	chr3:45952800-45963600	Weak transcription	Psoas Muscle	Psoas
19	chr3:45952800-45964600	Weak transcription	Fetal Heart	heart
20	chr3:45953200-45959600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:45953200-45960800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:45953400-45959800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:45955800-45960000	Weak transcription	Fetal Intestine Large	intestine
24	chr3:45956400-45959600	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:45956600-45960200	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr3:45956800-45961800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:45957400-45960800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:45957400-45961600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:45957400-45963000	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:45957600-45960000	Weak transcription	Fetal Lung	lung
31	chr3:45957600-45965000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:45957800-45960000	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:45957800-45960200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:45957800-45960200	Weak transcription	Left Ventricle	heart
35	chr3:45957800-45960800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:45957800-45961200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:45957800-45961400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:45957800-45962400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:45957800-45962600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:45957800-45962600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:45957800-45962600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:45957800-45963000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr3:45957800-45963000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:45957800-45963600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:45957800-45963600	Weak transcription	Colonic Mucosa	Colon
46	chr3:45957800-45969000	Weak transcription	K562	blood
47	chr3:45957800-45971200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:45958000-45959600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr3:45958000-45959800	Enhancers	GM12878-XiMat	blood
50	chr3:45958000-45960000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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