Variant report

Variant	rs12402165
Chromosome Location	chr1:179274781-179274782
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179261622..179263468-chr1:179274753..179276315,2	K562	blood:
2	chr1:179262649..179264550-chr1:179273241..179276604,3	K562	blood:
3	chr1:179273495..179275891-chr1:179281691..179283640,2	K562	blood:
4	chr1:179266790..179268502-chr1:179273763..179275636,2	K562	blood:

Variant related genes	Relation type
ENSG00000057252	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10753191	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs10798665	0.86[JPT][hapmap]
rs10913728	0.86[CHB][hapmap]
rs10913734	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs12022539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12026030	0.93[EUR][1000 genomes]
rs12028643	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12031894	0.99[EUR][1000 genomes]
rs12035050	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12039884	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12044039	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12045521	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12049122	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12049237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138619	0.81[JPT][hapmap]
rs12404921	0.99[EUR][1000 genomes]
rs12408349	1.00[CEU][hapmap];0.80[JPT][hapmap];0.97[EUR][1000 genomes]
rs12408668	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1475798	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16853917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16853936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17362081	0.95[CEU][hapmap]
rs2068234	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2152317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2636266	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs2636289	0.82[EUR][1000 genomes]
rs2636290	0.95[CEU][hapmap]
rs2793804	0.81[EUR][1000 genomes]
rs2793805	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs2793807	0.82[EUR][1000 genomes]
rs2793808	0.82[EUR][1000 genomes]
rs2816179	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816180	0.87[EUR][1000 genomes]
rs3753524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3753526	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs380951	0.86[EUR][1000 genomes]
rs3818433	0.95[CEU][hapmap]
rs413881	0.97[EUR][1000 genomes]
rs425858	0.86[EUR][1000 genomes]
rs4478776	0.86[EUR][1000 genomes]
rs58284152	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58948941	0.95[EUR][1000 genomes]
rs59777301	0.94[EUR][1000 genomes]
rs60595009	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61821690	0.82[EUR][1000 genomes]
rs61821735	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61821737	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61821738	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61821739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61821740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824363	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61824364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61824365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61824368	0.95[EUR][1000 genomes]
rs61824371	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61824388	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61824389	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6675772	0.99[EUR][1000 genomes]
rs6694339	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7414502	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs931441	0.95[CEU][hapmap]

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	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv990767	chr1:179270152-179277921	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179263800-179304600	Weak transcription	Lung	lung
2	chr1:179263800-179306400	Weak transcription	Gastric	stomach
3	chr1:179264000-179279600	Weak transcription	Fetal Brain Male	brain
4	chr1:179264200-179290200	Weak transcription	Aorta	Aorta
5	chr1:179264600-179275000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:179264600-179278600	Weak transcription	Colonic Mucosa	Colon
7	chr1:179264600-179281200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:179264600-179292000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:179264600-179304600	Weak transcription	Right Ventricle	heart
10	chr1:179264600-179310200	Weak transcription	Brain Substantia Nigra	brain
11	chr1:179264600-179314000	Weak transcription	Brain Angular Gyrus	brain
12	chr1:179264600-179314000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:179264800-179276200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:179264800-179276400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:179264800-179277800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:179264800-179278800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:179264800-179279400	Weak transcription	HSMMtube	muscle
18	chr1:179264800-179313800	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:179264800-179313800	Weak transcription	Fetal Brain Female	brain
20	chr1:179264800-179334200	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:179265000-179276200	Weak transcription	Osteobl	bone
22	chr1:179265400-179287600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:179266400-179276200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:179266400-179286400	Weak transcription	Fetal Kidney	kidney
25	chr1:179266400-179322800	Weak transcription	Small Intestine	intestine
26	chr1:179267800-179287000	Weak transcription	Spleen	Spleen
27	chr1:179268400-179278200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:179268400-179280200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:179268400-179312000	Weak transcription	Fetal Thymus	thymus
30	chr1:179269600-179280000	Weak transcription	Thymus	Thymus
31	chr1:179270200-179283200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:179270400-179277600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr1:179271000-179279000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr1:179271200-179275200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:179271200-179277600	Strong transcription	Liver	Liver
36	chr1:179271400-179276800	Strong transcription	Fetal Intestine Large	intestine
37	chr1:179271400-179277000	Strong transcription	Primary T cells from cord blood	blood
38	chr1:179271400-179277000	Strong transcription	Dnd41	blood
39	chr1:179271400-179277200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:179271400-179287600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:179271600-179274800	Strong transcription	GM12878-XiMat	blood
42	chr1:179271600-179275200	Genic enhancers	Hela-S3	cervix
43	chr1:179271600-179277000	Strong transcription	Primary B cells from cord blood	blood
44	chr1:179271600-179278200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:179271600-179283800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:179271600-179286400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:179271800-179276800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:179271800-179277000	Strong transcription	Primary B cells from peripheral blood	blood
49	chr1:179271800-179277400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:179271800-179280200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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