Variant report

Variant	rs3747998
Chromosome Location	chr1:114186138-114186139
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114185827..114187693-chr17:4268175..4270589,2	MCF-7	breast:
2	chr1:114185208..114187215-chr1:114207813..114209339,2	K562	blood:
3	chr1:114186046..114188816-chr1:114192338..114195071,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132388	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10127930	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10489936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1080307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217384	0.82[EUR][1000 genomes]
rs12723023	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12729708	0.82[EUR][1000 genomes]
rs12730675	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12730735	0.87[EUR][1000 genomes]
rs12731010	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12731969	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12734625	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12735104	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12739970	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12746609	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12748727	0.88[EUR][1000 genomes]
rs12752932	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12753075	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12753351	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12758546	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12760457	0.88[EUR][1000 genomes]
rs13374352	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17274550	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17274620	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17274634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17359302	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17462614	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17508163	0.82[ASN][1000 genomes]
rs17508814	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17509390	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1885454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2040040	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2359173	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2359174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34042871	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34258372	0.91[CEU][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34341173	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34649199	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34698891	0.92[EUR][1000 genomes]
rs34799402	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34857922	0.82[EUR][1000 genomes]
rs34877889	0.87[EUR][1000 genomes]
rs35320278	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35383900	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35836713	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36115604	0.88[EUR][1000 genomes]
rs3748003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3752953	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes]
rs3761931	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3789595	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789599	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap]
rs3789607	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3789609	0.87[EUR][1000 genomes]
rs4581284	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs55855422	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56257513	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61817579	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61817586	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61817617	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61819423	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61819424	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61820162	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6668829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6674848	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66782936	0.84[ASN][1000 genomes]
rs6703387	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7533391	0.82[EUR][1000 genomes]
rs7533605	0.88[EUR][1000 genomes]
rs7549685	0.86[EUR][1000 genomes]
rs7555354	0.88[EUR][1000 genomes]
rs9803891	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][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	nsv1012324	chr1:114135133-114206843	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv872161	chr1:114162194-114280135	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114159000-114195000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:114159200-114194800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:114161800-114199800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr1:114169200-114189400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:114171600-114241400	Weak transcription	Right Ventricle	heart
6	chr1:114172400-114192600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:114173000-114214400	Weak transcription	Esophagus	oesophagus
8	chr1:114173000-114226800	Weak transcription	Aorta	Aorta
9	chr1:114173600-114195000	Weak transcription	HMEC	breast
10	chr1:114173600-114206000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:114173800-114196200	Weak transcription	Gastric	stomach
12	chr1:114173800-114199600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:114173800-114201800	Weak transcription	Colonic Mucosa	Colon
14	chr1:114173800-114201800	Weak transcription	Lung	lung
15	chr1:114173800-114214400	Weak transcription	Pancreas	Pancrea
16	chr1:114173800-114236000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:114179800-114239600	Weak transcription	Spleen	Spleen
18	chr1:114181200-114199400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:114181800-114199800	Weak transcription	Fetal Brain Female	brain
20	chr1:114182000-114219600	Weak transcription	Fetal Kidney	kidney
21	chr1:114182200-114189200	Weak transcription	Placenta	Placenta
22	chr1:114182200-114197600	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:114182600-114187800	Weak transcription	Fetal Stomach	stomach
24	chr1:114182600-114189400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:114182600-114189400	Weak transcription	Osteobl	bone
26	chr1:114182600-114194800	Weak transcription	HSMM	muscle
27	chr1:114182600-114206200	Weak transcription	Hela-S3	cervix
28	chr1:114182800-114193600	Weak transcription	Fetal Intestine Small	intestine
29	chr1:114182800-114201800	Weak transcription	Brain Germinal Matrix	brain
30	chr1:114182800-114201800	Weak transcription	Fetal Brain Male	brain
31	chr1:114182800-114217400	Weak transcription	NHDF-Ad	bronchial
32	chr1:114183000-114196200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:114183000-114200000	Weak transcription	HSMMtube	muscle
34	chr1:114183000-114201200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:114183000-114235800	Weak transcription	Dnd41	blood
36	chr1:114183200-114199600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:114183400-114193600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:114183400-114195400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:114183400-114199800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:114183400-114215800	Weak transcription	Fetal Lung	lung
41	chr1:114183600-114199200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:114183600-114216400	Weak transcription	A549	lung
43	chr1:114183800-114186600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr1:114184000-114189600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:114184000-114189600	Weak transcription	Fetal Heart	heart
46	chr1:114184400-114188600	Strong transcription	Fetal Intestine Large	intestine
47	chr1:114184400-114199600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:114184600-114186600	Strong transcription	Liver	Liver
49	chr1:114184600-114186600	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:114184600-114186800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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