Variant report

Variant	rs476540
Chromosome Location	chr1:225779304-225779305
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225772554..225774967-chr1:225778509..225781013,2	MCF-7	breast:
2	chr1:225778437..225779968-chr1:225964469..225966570,2	K562	blood:
3	chr1:225779097..225781482-chr1:225782151..225783761,2	MCF-7	breast:
4	chr1:225778350..225780022-chr1:225784894..225787023,2	K562	blood:
5	chr1:225777393..225780281-chr1:225780667..225783094,2	K562	blood:
6	chr1:225777772..225779760-chr1:225795997..225798741,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143742	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10753406	0.84[EUR][1000 genomes]
rs10799317	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10799318	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10799319	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10915833	0.84[EUR][1000 genomes]
rs10915834	0.82[EUR][1000 genomes]
rs10915839	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10915847	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11584675	0.84[EUR][1000 genomes]
rs12028305	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2639703	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2639716	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2657564	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2657569	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2840958	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2840967	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2840968	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3820226	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3856156	0.84[EUR][1000 genomes]
rs4653643	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs487591	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs498350	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs510293	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs511649	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs516249	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs551996	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs554744	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs554992	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs561656	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs576861	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6426076	0.84[EUR][1000 genomes]
rs6668770	0.84[EUR][1000 genomes]
rs6702555	0.81[EUR][1000 genomes]
rs6751	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs712062	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7515907	0.84[EUR][1000 genomes]
rs7524766	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7540181	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7541598	0.84[EUR][1000 genomes]
rs7555139	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7555553	0.84[EUR][1000 genomes]
rs812523	0.87[ASN][1000 genomes]
rs9804142	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs476540	RP11-496N12.9	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225748800-225799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:225749200-225783800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:225759600-225787600	Weak transcription	Fetal Intestine Small	intestine
4	chr1:225760000-225820600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:225766400-225780000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:225766400-225783600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:225766600-225779600	Weak transcription	NH-A	brain
8	chr1:225768400-225781200	Weak transcription	Right Ventricle	heart
9	chr1:225768600-225787800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:225768800-225781000	Weak transcription	HSMM	muscle
11	chr1:225768800-225805600	Weak transcription	Aorta	Aorta
12	chr1:225769000-225783000	Weak transcription	HSMMtube	muscle
13	chr1:225769200-225779800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:225769200-225783200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:225769400-225779600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:225770000-225780000	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:225770000-225782000	Weak transcription	Right Atrium	heart
18	chr1:225770000-225783200	Weak transcription	Psoas Muscle	Psoas
19	chr1:225770000-225785200	Weak transcription	Left Ventricle	heart
20	chr1:225770000-225787600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:225770200-225779600	Weak transcription	Fetal Lung	lung
22	chr1:225770400-225780000	Weak transcription	Ovary	ovary
23	chr1:225770600-225779600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:225770600-225779800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:225770800-225781800	Weak transcription	Osteobl	bone
26	chr1:225771000-225779600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:225771000-225784000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:225774000-225780600	Weak transcription	Fetal Stomach	stomach
29	chr1:225774000-225781000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:225774800-225793200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:225775600-225781200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:225776200-225781400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:225776400-225797200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr1:225776800-225781000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr1:225777000-225779800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:225777000-225781000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:225777000-225781600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:225777000-225793400	Weak transcription	Pancreas	Pancrea
39	chr1:225777400-225781200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:225777800-225780800	Enhancers	Fetal Heart	heart
41	chr1:225777800-225783600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:225778200-225780800	Weak transcription	Fetal Brain Male	brain
43	chr1:225778400-225784000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:225778400-225784400	Weak transcription	Brain Angular Gyrus	brain
45	chr1:225778600-225779400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:225778600-225779600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr1:225778600-225779800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:225778600-225781200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:225778600-225783600	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:225778600-225785400	Weak transcription	Brain Cingulate Gyrus	brain

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