Variant report

Variant	rs2406974
Chromosome Location	chr4:152601841-152601842
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:152593842..152596396-chr4:152600528..152602296,2	K562	blood:
2	chr4:152601188..152603111-chr4:152604045..152605768,2	MCF-7	breast:
3	chr4:152587087..152588949-chr4:152600852..152602863,2	K562	blood:

Variant related genes	Relation type
ENSG00000251455	Chromatin interaction
ENSG00000251603	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10001603	0.86[EUR][1000 genomes]
rs10013612	0.82[EUR][1000 genomes]
rs10016160	0.82[EUR][1000 genomes]
rs10222838	0.82[EUR][1000 genomes]
rs10222925	0.82[EUR][1000 genomes]
rs11723227	0.82[EUR][1000 genomes]
rs12503677	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12641433	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12641438	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12641441	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12647420	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12647462	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12647465	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12647616	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1366907	0.82[EUR][1000 genomes]
rs1429558	0.82[EUR][1000 genomes]
rs1429559	0.82[EUR][1000 genomes]
rs17360371	0.80[EUR][1000 genomes]
rs17360385	0.84[EUR][1000 genomes]
rs1877185	0.82[EUR][1000 genomes]
rs1877186	0.82[EUR][1000 genomes]
rs1877188	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2089811	0.82[EUR][1000 genomes]
rs2175409	0.82[EUR][1000 genomes]
rs2406973	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28659854	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3805356	0.82[EUR][1000 genomes]
rs3828546	0.82[EUR][1000 genomes]
rs4696106	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4696107	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4696108	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4696110	0.84[EUR][1000 genomes]
rs4696286	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4696287	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4696290	0.88[EUR][1000 genomes]
rs58751443	0.81[EUR][1000 genomes]
rs59350867	0.82[EUR][1000 genomes]
rs6535816	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6535822	0.82[EUR][1000 genomes]
rs6816002	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6847844	0.82[EUR][1000 genomes]
rs6849111	0.81[EUR][1000 genomes]
rs6855883	0.82[EUR][1000 genomes]
rs6857073	0.82[EUR][1000 genomes]
rs7654294	0.82[EUR][1000 genomes]
rs7669465	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7669761	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7675818	0.82[EUR][1000 genomes]
rs9996320	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755535	chr4:152549395-152609395	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv4551	chr4:152582617-152627367	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1026511	chr4:152593382-152611915	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152563800-152625200	Weak transcription	Hela-S3	cervix
2	chr4:152567400-152608600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr4:152567800-152609000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:152581200-152602800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr4:152581200-152608400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr4:152585600-152628600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:152585800-152640400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr4:152586400-152609000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:152589200-152608800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr4:152589200-152619200	Weak transcription	Dnd41	blood
11	chr4:152590600-152609000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr4:152591200-152608600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr4:152591200-152646800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr4:152592200-152608000	Weak transcription	Thymus	Thymus
15	chr4:152592600-152636400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:152593600-152608000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:152593600-152608800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:152595200-152611600	Weak transcription	K562	blood
19	chr4:152595600-152602400	Weak transcription	HepG2	liver
20	chr4:152595600-152608600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:152596200-152608600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:152596200-152624000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr4:152596400-152604400	Weak transcription	Pancreas	Pancrea
24	chr4:152596400-152608000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:152596400-152608000	Weak transcription	Ovary	ovary
26	chr4:152596400-152608600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr4:152596400-152608600	Weak transcription	Placenta	Placenta
28	chr4:152596400-152609000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr4:152596400-152627800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr4:152596400-152628600	Weak transcription	Colonic Mucosa	Colon
31	chr4:152596400-152640600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr4:152596600-152604600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:152596600-152605400	Weak transcription	Stomach Mucosa	stomach
34	chr4:152596600-152608000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr4:152596600-152608000	Weak transcription	Right Atrium	heart
36	chr4:152596600-152608600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr4:152596800-152602600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:152596800-152602600	Weak transcription	Aorta	Aorta
39	chr4:152596800-152602600	Weak transcription	Esophagus	oesophagus
40	chr4:152596800-152602800	Weak transcription	Brain Anterior Caudate	brain
41	chr4:152596800-152606000	Weak transcription	Right Ventricle	heart
42	chr4:152596800-152606400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr4:152596800-152606400	Strong transcription	Primary T cells from cord blood	blood
44	chr4:152596800-152606400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:152596800-152607400	Weak transcription	Lung	lung
46	chr4:152596800-152607800	Weak transcription	Psoas Muscle	Psoas
47	chr4:152596800-152608000	Weak transcription	Fetal Lung	lung
48	chr4:152596800-152608800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr4:152597000-152604400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr4:152597000-152607200	Weak transcription	Stomach Smooth Muscle	stomach

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