Variant report

Variant	rs4708042
Chromosome Location	chr6:73975404-73975405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:73972509-73976913	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:73962925..73964813-chr6:73974768..73977580,2	K562	blood:
2	chr6:73968889..73971935-chr6:73973198..73976161,3	K562	blood:
3	chr6:73970435..73971985-chr6:73974301..73976161,2	K562	blood:

Variant related genes	Relation type
ENSG00000243501	TF binding region
KHDC1	TF binding region
ENSG00000229852	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10455092	0.89[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10455273	0.92[ASN][1000 genomes]
rs10455274	0.92[ASN][1000 genomes]
rs1066687	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12153835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12203663	0.92[ASN][1000 genomes]
rs12208781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12210531	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12216162	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12526643	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12529624	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12529658	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12530029	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12530079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13194683	0.91[ASN][1000 genomes]
rs13212903	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13213885	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13219250	0.92[ASN][1000 genomes]
rs1555443	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1869559	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1970551	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1974368	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2124004	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2124006	0.89[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2168113	0.89[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2254630	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2603471	0.83[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2797086	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28530192	0.92[ASN][1000 genomes]
rs2984129	0.92[ASN][1000 genomes]
rs34246858	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34531450	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34637067	0.92[ASN][1000 genomes]
rs34821383	0.92[ASN][1000 genomes]
rs35664677	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4706533	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4706534	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708041	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471270	0.96[ASN][1000 genomes]
rs471938	0.92[ASN][1000 genomes]
rs502107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs502282	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs509406	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs510551	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs511219	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs512366	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555779	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs57113415	0.83[ASN][1000 genomes]
rs573535	0.92[ASN][1000 genomes]
rs576229	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs579736	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs61493410	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62438232	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62438233	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62438235	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62438239	0.92[ASN][1000 genomes]
rs66984567	0.92[ASN][1000 genomes]
rs6923111	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6923734	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7382700	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7740081	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742847	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7743609	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7744174	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753960	0.81[GIH][hapmap]
rs7758047	0.94[ASN][1000 genomes]
rs7759043	0.94[ASN][1000 genomes]
rs7759315	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7764719	0.91[ASN][1000 genomes]
rs7765618	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769905	0.95[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs9800483	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9800824	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1022151	chr6:73876795-73996828	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv538304	chr6:73876795-73996828	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1030079	chr6:73920050-73984084	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4708042	EIF3EP1	cis	Skin Sun Exposed Lower leg	GTEx
rs4708042	IMPG1	cis	parietal	SCAN
rs4708042	KHDC1	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73973400-73985000	Weak transcription	Small Intestine	intestine
2	chr6:73973400-73986400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:73973400-74000400	Weak transcription	Aorta	Aorta
4	chr6:73973600-73976400	Weak transcription	HSMMtube	muscle
5	chr6:73973600-73978000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:73973600-73978400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr6:73973600-73983400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr6:73973600-73984400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:73973600-73985400	Weak transcription	Left Ventricle	heart
10	chr6:73973600-74018600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:73973600-74018600	Weak transcription	A549	lung
12	chr6:73973600-74018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:73973800-73976400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:73973800-73976400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:73973800-73976800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:73973800-73977600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr6:73973800-73978000	Weak transcription	Fetal Intestine Small	intestine
18	chr6:73973800-73980600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:73973800-73983400	Weak transcription	Placenta	Placenta
20	chr6:73973800-73985200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:73973800-73995600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:73973800-73995600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:73973800-74000400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr6:73974000-73980600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:73974000-73980600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:73974000-73983800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr6:73974000-73983800	Weak transcription	Osteobl	bone
28	chr6:73974000-73985000	Weak transcription	Lung	lung
29	chr6:73974000-73995600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:73974000-74000400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:73974000-74009000	Weak transcription	HSMM	muscle
32	chr6:73974000-74018400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr6:73974200-73978600	Weak transcription	Brain Substantia Nigra	brain
34	chr6:73974200-73983400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr6:73974200-73992600	Weak transcription	Colon Smooth Muscle	Colon
36	chr6:73974400-73975800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr6:73974400-73977200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:73974400-73977600	Weak transcription	Fetal Brain Female	brain
39	chr6:73974400-73977800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:73974400-73977800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:73974400-73977800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:73974400-73980800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:73974400-73983600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr6:73974400-73983600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:73974400-73983600	Weak transcription	Ovary	ovary
46	chr6:73974400-73984000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:73974400-73986000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr6:73974400-73986200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr6:73974400-73986600	Weak transcription	Pancreas	Pancrea
50	chr6:73974400-73986800	Weak transcription	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links