Variant report

Variant	rs7246368
Chromosome Location	chr19:39157599-39157600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39136593..39141523-chr19:39155434..39158627,5	K562	blood:
2	chr19:39156656..39158268-chr19:39339409..39341724,2	MCF-7	breast:
3	chr19:39157029..39159931-chr19:39175100..39177737,2	K562	blood:
4	chr19:39156222..39158028-chr19:39160453..39162596,3	K562	blood:
5	chr19:39156941..39159370-chr19:39200344..39202279,2	MCF-7	breast:
6	chr19:39156254..39158028-chr19:39160745..39162596,2	K562	blood:
7	chr19:39157020..39159393-chr19:39170595..39173839,3	MCF-7	breast:
8	chr19:39156320..39158010-chr19:39194511..39197034,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000104824	Chromatin interaction
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1106372	0.80[AFR][1000 genomes]
rs12971309	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12972997	0.80[AFR][1000 genomes]
rs12974733	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12975079	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12975256	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12976598	0.80[AFR][1000 genomes]
rs12977238	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12977599	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12978715	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12978914	0.84[AFR][1000 genomes]
rs12979947	0.82[ASN][1000 genomes]
rs12980399	0.80[AFR][1000 genomes]
rs12981131	0.82[ASN][1000 genomes]
rs12981984	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12984794	0.83[EUR][1000 genomes]
rs12985030	0.80[AFR][1000 genomes]
rs12985558	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12986121	0.84[AFR][1000 genomes]
rs12986337	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs17589359	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2086148	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2126970	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2279145	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2279146	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2287728	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34026184	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs34082501	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs34083318	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34105297	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34126343	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs34134906	0.82[ASN][1000 genomes]
rs34332511	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34368672	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs34525537	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34558140	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34563817	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs34592527	0.92[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	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs34843929	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs34862518	0.83[EUR][1000 genomes]
rs34899634	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35074956	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35096737	0.80[AFR][1000 genomes]
rs35193699	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35281901	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs35436155	0.80[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	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35640008	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35666464	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35685980	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35691365	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35716073	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35729716	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35807146	0.84[AFR][1000 genomes]
rs35856174	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35941349	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3786840	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs56946356	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60454376	0.83[EUR][1000 genomes]
rs61121905	0.80[AFR][1000 genomes]
rs62119101	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62119102	0.83[EUR][1000 genomes]
rs62119103	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62119105	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62119109	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62119116	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62120068	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs62121763	0.84[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	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62121827	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62121828	0.88[AFR][1000 genomes]
rs62121829	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs71356822	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7248577	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7260070	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs8105055	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs8105069	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs8105080	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs8105216	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs8105550	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs899199	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs899200	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv960837	chr19:39156364-39162333	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7246368	EIF3K	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
2	chr19:39147400-39160000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:39147800-39160800	Enhancers	Placenta	Placenta
4	chr19:39149600-39160200	Enhancers	Pancreas	Pancrea
5	chr19:39150000-39157600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
6	chr19:39151200-39157600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr19:39151200-39157600	Genic enhancers	Fetal Stomach	stomach
8	chr19:39151400-39160000	Enhancers	H9 Cell Line	embryonic stem cell
9	chr19:39152000-39159800	Weak transcription	Dnd41	blood
10	chr19:39152400-39159200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:39152400-39160000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr19:39152600-39157600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:39152600-39157600	Enhancers	Fetal Lung	lung
14	chr19:39152600-39158400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:39152600-39158600	Enhancers	Ovary	ovary
16	chr19:39152600-39159200	Enhancers	Colonic Mucosa	Colon
17	chr19:39152600-39160000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr19:39152600-39160000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr19:39152600-39162200	Enhancers	Spleen	Spleen
20	chr19:39152600-39164000	Enhancers	Liver	Liver
21	chr19:39152800-39157600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:39152800-39157600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr19:39152800-39159400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr19:39152800-39161200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:39153000-39158000	Enhancers	Gastric	stomach
26	chr19:39153000-39158400	Enhancers	Primary B cells from cord blood	blood
27	chr19:39153000-39158600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:39153000-39161200	Enhancers	Placenta Amnion	Placenta Amnion
29	chr19:39153200-39159200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:39153400-39159400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:39153400-39161200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr19:39154000-39158800	Transcr. at gene 5' and 3'	A549	lung
33	chr19:39154000-39160200	Enhancers	Primary hematopoietic stem cells	blood
34	chr19:39154000-39160400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
35	chr19:39154000-39162600	Enhancers	Fetal Kidney	kidney
36	chr19:39154000-39162800	Enhancers	Small Intestine	intestine
37	chr19:39154200-39158000	Bivalent Enhancer	Fetal Thymus	thymus
38	chr19:39154200-39158600	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr19:39154200-39160000	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr19:39154200-39162600	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr19:39154400-39157600	Enhancers	Fetal Brain Male	brain
42	chr19:39154400-39160200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:39154400-39161200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr19:39154600-39158000	Enhancers	Lung	lung
45	chr19:39154600-39158200	Enhancers	Primary B cells from peripheral blood	blood
46	chr19:39154600-39158800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:39154600-39159000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:39154600-39159000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr19:39154600-39162000	Enhancers	Left Ventricle	heart
50	chr19:39154600-39163000	Enhancers	Right Atrium	heart

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