Variant report

Variant	rs12493471
Chromosome Location	chr3:45951678-45951679
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45944264..45946380-chr3:45950311..45953306,2	MCF-7	breast:
2	chr3:45948084..45950746-chr3:45951152..45952829,2	K562	blood:

Variant related genes	Relation type
ENSG00000201635	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs7652331	0.87[CEU][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.88[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12493471	FYCO1	cis	lung	GTEx
rs12493471	CDC25A	cis	cerebellum	SCAN
rs12493471	SACM1L	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

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	chr3:45941200-45952400	Weak transcription	Psoas Muscle	Psoas
5	chr3:45941400-45960000	Weak transcription	Adipose Nuclei	Adipose
6	chr3:45943000-45961000	Weak transcription	Brain Substantia Nigra	brain
7	chr3:45943600-45961200	Weak transcription	Gastric	stomach
8	chr3:45946200-45956800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:45946200-45960400	Weak transcription	Aorta	Aorta
10	chr3:45947000-45960200	Weak transcription	Lung	lung
11	chr3:45947800-45956800	Transcr. at gene 5' and 3'	Dnd41	blood
12	chr3:45948200-45961000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:45948400-45961600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:45948800-45951800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:45948800-45960200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:45949200-45962400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:45949400-45958400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:45949800-45956800	Weak transcription	Small Intestine	intestine
19	chr3:45949800-45957400	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:45949800-45962600	Weak transcription	HepG2	liver
21	chr3:45950000-45952400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:45950000-45952800	Enhancers	Primary B cells from cord blood	blood
23	chr3:45950000-45953600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:45950000-45957600	Weak transcription	Esophagus	oesophagus
25	chr3:45950000-45960800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:45950200-45952600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:45950200-45952600	Weak transcription	K562	blood
28	chr3:45950200-45953200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:45950200-45953800	Weak transcription	HSMM	muscle
30	chr3:45950200-45954600	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
31	chr3:45950200-45955400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr3:45950200-45957000	Weak transcription	HSMMtube	muscle
33	chr3:45950200-45957600	Weak transcription	Colonic Mucosa	Colon
34	chr3:45950200-45959800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:45950200-45960000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:45950200-45960400	Weak transcription	Pancreas	Pancrea
37	chr3:45950400-45957200	Weak transcription	Left Ventricle	heart
38	chr3:45950400-45958800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:45950600-45951800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:45950600-45952200	Weak transcription	Fetal Heart	heart
41	chr3:45950600-45953000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:45950600-45955600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr3:45950600-45956200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr3:45950600-45956200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:45950600-45956200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr3:45950600-45956200	Weak transcription	Spleen	Spleen
47	chr3:45950800-45952400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr3:45950800-45952400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:45950800-45952800	Transcr. at gene 5' and 3'	Thymus	Thymus
50	chr3:45950800-45955600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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