Variant report

Variant	rs3778624
Chromosome Location	chr6:30302600-30302601
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30298070..30301347-chr6:30302009..30303774,3	MCF-7	breast:
2	chr6:30300818..30303385-chr6:30311181..30313582,3	MCF-7	breast:
3	chr6:30301782..30303711-chr6:30308127..30310894,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241370	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1045251	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1060065	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1264616	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1473102	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2023476	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2023477	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2023478	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2057727	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074474	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2097773	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2285798	0.81[ASN][1000 genomes]
rs2394779	0.81[ASN][1000 genomes]
rs2394780	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516697	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2516699	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2516700	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2516702	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2516704	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2516705	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2516706	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516707	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2516710	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2516713	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2523737	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523744	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2523745	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2523746	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2523747	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2523748	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2523750	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs261943	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs261948	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs261949	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28360021	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28360023	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844752	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844761	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844763	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844765	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2894145	0.80[ASN][1000 genomes]
rs3778626	0.83[ASN][1000 genomes]
rs6904208	0.82[AFR][1000 genomes]
rs6912239	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6912495	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7452694	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767653	0.82[AFR][1000 genomes]
rs7767817	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295843	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295844	0.82[ASN][1000 genomes]
rs9357095	0.81[ASN][1000 genomes]
rs9366755	0.81[ASN][1000 genomes]
rs9368628	0.81[ASN][1000 genomes]
rs9368632	0.81[ASN][1000 genomes]
rs9368633	0.81[ASN][1000 genomes]
rs9380168	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9380174	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9391679	0.81[ASN][1000 genomes]
rs9391806	0.81[ASN][1000 genomes]
rs9391807	0.81[ASN][1000 genomes]
rs9393999	0.81[ASN][1000 genomes]
rs9394000	0.81[ASN][1000 genomes]
rs9394001	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9394002	0.83[ASN][1000 genomes]
rs9394003	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs962899	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs974963	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[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	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3778624	LOC401245	cis	multi-tissue	Pritchard
rs3778624	HCG18	cis	normal skin	skin_eQTL
rs3778624	TRIM26	Cis_1M	lymphoblastoid	RTeQTL
rs3778624	HCG18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:128 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30295400-30303400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:30295400-30309400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:30295600-30303400	Weak transcription	Psoas Muscle	Psoas
4	chr6:30295600-30312600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:30295600-30312600	Weak transcription	Right Atrium	heart
6	chr6:30295600-30313000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:30295800-30303200	Weak transcription	NHDF-Ad	bronchial
8	chr6:30295800-30303400	Weak transcription	A549	lung
9	chr6:30295800-30311000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:30295800-30312400	Weak transcription	Fetal Heart	heart
11	chr6:30295800-30312400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:30296200-30310400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:30296600-30310600	Strong transcription	Primary B cells from peripheral blood	blood
14	chr6:30296800-30310000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:30296800-30310000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:30296800-30310200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:30296800-30310400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr6:30296800-30310600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:30296800-30310800	Strong transcription	Fetal Brain Female	brain
20	chr6:30296800-30311200	Strong transcription	Placenta	Placenta
21	chr6:30296800-30311400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:30296800-30311800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:30297000-30304200	Strong transcription	Ovary	ovary
24	chr6:30297000-30305000	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:30297000-30306000	Strong transcription	HSMM	muscle
26	chr6:30297000-30306200	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr6:30297000-30307800	Strong transcription	Osteobl	bone
28	chr6:30297000-30310000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr6:30297000-30310200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:30297000-30310200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr6:30297000-30310400	Strong transcription	Brain Cingulate Gyrus	brain
32	chr6:30297000-30310600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr6:30297000-30311000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:30297200-30304600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr6:30297200-30305800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:30297200-30306000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:30297200-30310200	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:30297200-30310200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:30297200-30310200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:30297200-30310200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr6:30297200-30310200	Strong transcription	NHEK	skin
42	chr6:30297200-30310400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:30297200-30310400	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr6:30297200-30310400	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr6:30297200-30310600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr6:30297200-30310600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr6:30297200-30310800	Strong transcription	Liver	Liver
48	chr6:30297200-30310800	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr6:30297200-30310800	Strong transcription	Stomach Smooth Muscle	stomach
50	chr6:30297200-30311000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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