Variant report

Variant	rs7260070
Chromosome Location	chr19:39162435-39162436
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39160838..39163402-chr19:39174691..39176835,2	MCF-7	breast:
2	chr19:39156222..39158028-chr19:39160453..39162596,3	K562	blood:
3	chr19:39152656..39156169-chr19:39159383..39162487,4	K562	blood:
4	chr19:39149024..39154711-chr19:39158901..39163144,7	MCF-7	breast:
5	chr19:39161055..39163275-chr19:39172924..39175598,3	K562	blood:
6	chr19:39156254..39158028-chr19:39160745..39162596,2	K562	blood:
7	chr19:39161163..39163302-chr19:39198153..39200836,2	K562	blood:

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1106372	0.88[AFR][1000 genomes]
rs12971309	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12972987	0.85[AFR][1000 genomes]
rs12972997	0.88[AFR][1000 genomes]
rs12974733	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12975079	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12975256	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12976598	0.88[AFR][1000 genomes]
rs12977238	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12977599	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12978273	0.85[AFR][1000 genomes]
rs12978715	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12978914	0.92[AFR][1000 genomes]
rs12979947	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12980399	0.88[AFR][1000 genomes]
rs12981131	0.82[ASN][1000 genomes]
rs12981984	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12983550	0.85[AFR][1000 genomes]
rs12984794	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12985030	0.88[AFR][1000 genomes]
rs12985558	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12985871	0.85[AFR][1000 genomes]
rs12986032	0.85[AFR][1000 genomes]
rs12986121	0.92[AFR][1000 genomes]
rs12986337	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs17589359	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2001856	0.85[AFR][1000 genomes]
rs2086148	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2126970	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2279145	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2279146	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2287728	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34026184	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs34082501	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs34083318	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34105297	0.96[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34126343	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs34134906	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs34332511	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34368672	0.96[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs34525537	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34558140	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34563817	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs34592527	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs34695688	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34703567	0.82[ASN][1000 genomes]
rs34717167	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs34843929	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs34862518	0.83[EUR][1000 genomes]
rs34899634	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs34911882	0.85[AFR][1000 genomes]
rs35007285	0.85[AFR][1000 genomes]
rs35074956	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35096737	0.88[AFR][1000 genomes]
rs35193699	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35281901	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs35436155	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35488280	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35576862	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35640008	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35666464	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35685980	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35691365	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35716073	0.96[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35729716	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35807146	0.92[AFR][1000 genomes]
rs35855940	0.85[AFR][1000 genomes]
rs35856174	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35941349	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3786840	0.96[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs45599933	0.85[AFR][1000 genomes]
rs56817884	0.83[AFR][1000 genomes]
rs56946356	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60454376	0.83[EUR][1000 genomes]
rs61121905	0.88[AFR][1000 genomes]
rs62119101	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62119102	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62119103	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62119105	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62119109	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62119116	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62120068	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs62120072	0.85[AFR][1000 genomes]
rs62120074	0.85[AFR][1000 genomes]
rs62120159	0.88[AFR][1000 genomes]
rs62121763	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62121764	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62121811	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121819	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62121821	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62121823	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62121827	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62121828	0.96[AFR][1000 genomes]
rs62121829	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs71356822	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7246368	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248577	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs732135	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8103530	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8104815	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs8105055	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs8105069	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs8105080	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs8105216	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs8105550	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs899199	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs899200	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7260070	EIF3K	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
2	chr19:39152600-39164000	Enhancers	Liver	Liver
3	chr19:39154000-39162600	Enhancers	Fetal Kidney	kidney
4	chr19:39154000-39162800	Enhancers	Small Intestine	intestine
5	chr19:39154200-39162600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr19:39154600-39163000	Enhancers	Right Atrium	heart
7	chr19:39154800-39163000	Genic enhancers	Fetal Intestine Small	intestine
8	chr19:39155000-39162800	Genic enhancers	Fetal Intestine Large	intestine
9	chr19:39155200-39162800	Enhancers	Brain Angular Gyrus	brain
10	chr19:39155200-39163800	Genic enhancers	NHEK	skin
11	chr19:39155400-39162800	Enhancers	Brain Hippocampus Middle	brain
12	chr19:39155400-39162800	Enhancers	Brain Substantia Nigra	brain
13	chr19:39156000-39162800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:39156400-39162800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:39156600-39164800	Enhancers	Fetal Heart	heart
16	chr19:39157800-39162600	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr19:39157800-39162600	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr19:39158000-39162800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr19:39158200-39162800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr19:39158200-39162800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr19:39158400-39162600	Genic enhancers	HMEC	breast
22	chr19:39158600-39162600	Enhancers	Primary B cells from peripheral blood	blood
23	chr19:39158600-39162800	Genic enhancers	Osteobl	bone
24	chr19:39158800-39162800	Enhancers	Adipose Nuclei	Adipose
25	chr19:39158800-39162800	Enhancers	Colon Smooth Muscle	Colon
26	chr19:39158800-39167600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:39159000-39165000	Weak transcription	Hela-S3	cervix
28	chr19:39159000-39166600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:39159000-39166800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr19:39159200-39162600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:39159400-39162800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:39159600-39162800	Enhancers	H1 Cell Line	embryonic stem cell
33	chr19:39159600-39162800	Enhancers	Aorta	Aorta
34	chr19:39159600-39162800	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr19:39159600-39169600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:39160000-39162800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:39160000-39162800	Enhancers	Brain Cingulate Gyrus	brain
38	chr19:39160000-39162800	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr19:39160200-39162800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:39160400-39162800	Enhancers	H9 Cell Line	embryonic stem cell
41	chr19:39160400-39162800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:39160400-39163000	Enhancers	Brain Anterior Caudate	brain
43	chr19:39160400-39163000	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr19:39160400-39173400	Weak transcription	Brain Germinal Matrix	brain
45	chr19:39160600-39162600	Enhancers	Primary T cells fromperipheralblood	blood
46	chr19:39160600-39162800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr19:39160600-39162800	Enhancers	Stomach Mucosa	stomach
48	chr19:39160600-39162800	Enhancers	NH-A	brain
49	chr19:39160600-39165200	Weak transcription	Dnd41	blood
50	chr19:39160800-39163200	Enhancers	Ovary	ovary

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