Variant report

Variant	rs6694339
Chromosome Location	chr1:179282939-179282940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179261306..179262860-chr1:179282015..179283875,2	K562	blood:
2	chr1:179280761..179283262-chr1:179333653..179335504,2	K562	blood:
3	chr1:179282159..179283986-chr1:179286549..179288130,2	K562	blood:
4	chr1:179273495..179275891-chr1:179281691..179283640,2	K562	blood:
5	chr1:179282486..179284547-chr1:179286630..179289373,2	K562	blood:

Variant related genes	Relation type
ENSG00000162779	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12022539	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12026030	0.88[EUR][1000 genomes]
rs12028643	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12031894	0.94[EUR][1000 genomes]
rs12035050	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12039884	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12044039	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12045521	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12049122	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12049237	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12402165	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12404921	0.94[EUR][1000 genomes]
rs12408349	0.91[EUR][1000 genomes]
rs12408668	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1475798	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16853917	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16853936	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2068234	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2152317	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2816179	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816180	0.83[EUR][1000 genomes]
rs3753524	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs380951	0.81[EUR][1000 genomes]
rs413881	0.91[EUR][1000 genomes]
rs425858	0.81[EUR][1000 genomes]
rs4478776	0.81[EUR][1000 genomes]
rs58284152	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58948941	0.99[EUR][1000 genomes]
rs59777301	0.88[EUR][1000 genomes]
rs60595009	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61821735	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61821737	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61821738	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61821739	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61821740	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61824363	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61824364	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61824365	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61824368	0.90[EUR][1000 genomes]
rs61824371	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61824388	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61824389	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6675772	0.94[EUR][1000 genomes]
rs7414502	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:98 , 50 per page) page: 1 2

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	chr1:179264200-179290200	Weak transcription	Aorta	Aorta
4	chr1:179264600-179292000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:179264600-179304600	Weak transcription	Right Ventricle	heart
6	chr1:179264600-179310200	Weak transcription	Brain Substantia Nigra	brain
7	chr1:179264600-179314000	Weak transcription	Brain Angular Gyrus	brain
8	chr1:179264600-179314000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:179264800-179313800	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:179264800-179313800	Weak transcription	Fetal Brain Female	brain
11	chr1:179264800-179334200	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:179265400-179287600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:179266400-179286400	Weak transcription	Fetal Kidney	kidney
14	chr1:179266400-179322800	Weak transcription	Small Intestine	intestine
15	chr1:179267800-179287000	Weak transcription	Spleen	Spleen
16	chr1:179268400-179312000	Weak transcription	Fetal Thymus	thymus
17	chr1:179270200-179283200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:179271400-179287600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:179271600-179283800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:179271600-179286400	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:179271800-179287600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:179272000-179284400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:179272000-179286000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:179272600-179288200	Weak transcription	Stomach Mucosa	stomach
25	chr1:179272600-179313800	Weak transcription	Brain Anterior Caudate	brain
26	chr1:179273000-179311600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:179273200-179290400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:179273200-179294600	Weak transcription	Placenta	Placenta
29	chr1:179273400-179287000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:179273800-179293400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:179274400-179289400	Weak transcription	Fetal Lung	lung
32	chr1:179274600-179284200	Weak transcription	Fetal Intestine Small	intestine
33	chr1:179274600-179302400	Weak transcription	Left Ventricle	heart
34	chr1:179274600-179304400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr1:179274600-179306000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:179275600-179311600	Weak transcription	HUVEC	blood vessel
37	chr1:179276400-179306200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr1:179276600-179283200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:179276600-179304800	Weak transcription	Pancreas	Pancrea
40	chr1:179276800-179284200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:179276800-179287000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:179276800-179290200	Weak transcription	Fetal Intestine Large	intestine
43	chr1:179276800-179295200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:179277000-179290400	Weak transcription	Dnd41	blood
45	chr1:179277000-179291600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:179277200-179288600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:179277600-179283000	Weak transcription	Liver	Liver
48	chr1:179277600-179288400	Weak transcription	Fetal Stomach	stomach
49	chr1:179277600-179296400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:179279400-179283200	Strong transcription	HepG2	liver

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