Variant report

Variant	rs34558140
Chromosome Location	chr19:39165407-39165408
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39148867..39151861-chr19:39164065..39166508,2	K562	blood:
2	chr19:39138117..39140492-chr19:39163770..39166162,3	K562	blood:
3	chr19:39164829..39167180-chr19:39341258..39342878,2	MCF-7	breast:
4	chr19:39163941..39166485-chr19:39290106..39293059,2	K562	blood:
5	chr19:39164276..39166665-chr19:39166865..39169150,2	K562	blood:

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1106372	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12971309	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12972987	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12972997	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12974733	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12975079	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12975256	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12975953	0.87[AMR][1000 genomes]
rs12976598	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12977238	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12977599	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12978273	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12978715	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12978914	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12979947	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12980399	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12981131	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12981984	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12983550	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12984794	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12985030	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12985558	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12985871	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12986032	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12986121	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12986337	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17589359	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2001856	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2086148	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2126970	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2279145	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2279146	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2287728	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34026184	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34054765	0.91[AMR][1000 genomes]
rs34082501	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34083318	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34105297	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34126343	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34134906	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34305426	0.91[AMR][1000 genomes]
rs34332511	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34368672	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34525537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34563817	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34592527	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34695688	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34703567	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34717167	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34843929	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34862518	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34899634	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34911882	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35007285	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35074956	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35096737	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs35134120	0.82[AMR][1000 genomes]
rs35193699	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35281901	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35403788	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35436155	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35488280	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35576862	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35640008	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35666464	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35685980	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35691365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35716073	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35729716	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35807146	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35855940	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs35856174	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35941349	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3786840	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs45599933	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56817884	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs56946356	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57230275	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60454376	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61121905	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs62119101	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62119102	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62119103	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62119105	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62119109	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62119116	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62120068	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62120072	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62120074	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62120159	0.88[AFR][1000 genomes]
rs62121763	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62121764	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62121811	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62121819	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121821	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62121823	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62121827	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62121828	0.96[AFR][1000 genomes]
rs62121829	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71356822	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7246368	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7248577	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7260070	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs732135	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8103530	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104815	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8105055	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8105069	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8105080	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8105216	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8105550	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs899199	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs899200	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs973009	0.84[ASN][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
rs34558140	EIF3K	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39158800-39167600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr19:39159000-39166600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr19:39159000-39166800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:39159600-39169600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr19:39160400-39173400	Weak transcription	Brain Germinal Matrix	brain
6	chr19:39161000-39166800	Weak transcription	Primary T cells from cord blood	blood
7	chr19:39161200-39166000	Weak transcription	Primary B cells from cord blood	blood
8	chr19:39161200-39176000	Weak transcription	Fetal Brain Male	brain
9	chr19:39161200-39176000	Weak transcription	Fetal Brain Female	brain
10	chr19:39162200-39173400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:39162400-39172000	Enhancers	Left Ventricle	heart
12	chr19:39162600-39169400	Genic enhancers	A549	lung
13	chr19:39162800-39165600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr19:39162800-39169400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr19:39162800-39173200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:39163200-39165800	Weak transcription	Ovary	ovary
17	chr19:39163800-39167600	Enhancers	Placenta	Placenta
18	chr19:39164400-39167600	Enhancers	Adipose Nuclei	Adipose
19	chr19:39164400-39172600	Enhancers	Small Intestine	intestine
20	chr19:39164400-39200200	Genic enhancers	Fetal Intestine Small	intestine
21	chr19:39164600-39165600	Genic enhancers	Fetal Muscle Leg	muscle
22	chr19:39164600-39165600	Enhancers	Spleen	Spleen
23	chr19:39164600-39166000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr19:39164600-39166200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:39164600-39166800	Enhancers	Stomach Mucosa	stomach
26	chr19:39164600-39167200	Enhancers	Fetal Intestine Large	intestine
27	chr19:39164600-39167400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr19:39164600-39167400	Enhancers	Lung	lung
29	chr19:39164600-39167600	Enhancers	Brain Substantia Nigra	brain
30	chr19:39164600-39167600	Enhancers	Right Ventricle	heart
31	chr19:39164600-39167800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr19:39164600-39167800	Enhancers	Fetal Lung	lung
33	chr19:39164600-39168000	Genic enhancers	Fetal Stomach	stomach
34	chr19:39164600-39170400	Enhancers	Right Atrium	heart
35	chr19:39164600-39170800	Genic enhancers	Osteobl	bone
36	chr19:39164600-39173800	Genic enhancers	HepG2	liver
37	chr19:39164600-39178200	Enhancers	Primary T cells fromperipheralblood	blood
38	chr19:39164800-39165600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:39164800-39165600	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr19:39164800-39165600	Genic enhancers	Rectal Smooth Muscle	rectum
41	chr19:39164800-39165600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr19:39164800-39165600	Flanking Active TSS	GM12878-XiMat	blood
43	chr19:39164800-39165600	Genic enhancers	HUVEC	blood vessel
44	chr19:39164800-39165800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr19:39164800-39165800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr19:39164800-39165800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr19:39164800-39166000	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr19:39164800-39166000	Enhancers	Fetal Kidney	kidney
49	chr19:39164800-39166000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr19:39164800-39166000	Flanking Active TSS	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links