Variant report

Variant	rs7744174
Chromosome Location	chr6:73973880-73973881
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	Cell Stage
1	chr6:73972686..73974360-chr6:74230027..74232988,2	MCF-7	breast:
2	chr6:73968889..73971935-chr6:73973198..73976161,3	K562	blood:

Variant related genes	Relation type
KHDC1	TF binding region
ENSG00000243501	TF binding region
ENSG00000229852	TF binding region
ENSG00000156508	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10455092	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[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12203663	0.92[ASN][1000 genomes]
rs12208781	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12210531	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12216162	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12526643	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12529624	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12529658	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12530029	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12530079	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13194683	0.91[ASN][1000 genomes]
rs13212903	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13213885	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13219250	0.92[ASN][1000 genomes]
rs1555443	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1869559	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1970551	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1974368	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2124004	0.91[ASN][1000 genomes]
rs2124006	0.84[ASN][1000 genomes]
rs2168113	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2254630	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2603471	0.96[ASN][1000 genomes]
rs2797086	0.85[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	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34531450	0.96[AFR][1000 genomes];0.89[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	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4706533	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4706534	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708041	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708042	0.91[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	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs502282	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs509406	0.85[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	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs512366	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555779	0.91[ASN][1000 genomes]
rs57113415	0.83[ASN][1000 genomes]
rs573535	0.92[ASN][1000 genomes]
rs576229	0.90[ASN][1000 genomes]
rs579736	0.96[ASN][1000 genomes]
rs61493410	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62438232	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62438233	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62438235	0.98[AFR][1000 genomes];0.89[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	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6923734	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7382700	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7740081	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742847	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7743609	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7758047	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7759043	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7759315	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7764719	0.91[ASN][1000 genomes]
rs7765618	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769905	0.86[ASN][1000 genomes]
rs9800483	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9800824	0.94[AFR][1000 genomes];0.92[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7744174	RP11-398K22.12	cis	Skin Sun Exposed Lower leg	GTEx
rs7744174	EIF3EP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73971800-73974000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:73971800-73974000	Active TSS	Brain Cingulate Gyrus	brain
3	chr6:73971800-73974600	Active TSS	Brain Angular Gyrus	brain
4	chr6:73972000-73974600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:73972200-73974000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:73972200-73974200	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr6:73972400-73974000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:73972400-73974200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr6:73972600-73974000	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr6:73972600-73974000	Active TSS	Muscle Satellite Cultured Cells	--
11	chr6:73972600-73974800	Enhancers	Stomach Mucosa	stomach
12	chr6:73973000-73974200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:73973000-73974200	Flanking Active TSS	HMEC	breast
14	chr6:73973000-73974400	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr6:73973200-73974000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:73973200-73974200	Flanking Active TSS	GM12878-XiMat	blood
17	chr6:73973200-73974400	Flanking Active TSS	Brain Germinal Matrix	brain
18	chr6:73973200-73975000	Flanking Active TSS	NHEK	skin
19	chr6:73973400-73974000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:73973400-73974000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr6:73973400-73974000	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr6:73973400-73974000	Flanking Active TSS	Fetal Brain Female	brain
23	chr6:73973400-73974000	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr6:73973400-73974000	Flanking Active TSS	Dnd41	blood
25	chr6:73973400-73974200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:73973400-73974200	Weak transcription	Gastric	stomach
27	chr6:73973400-73974400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr6:73973400-73974400	Enhancers	Pancreas	Pancrea
29	chr6:73973400-73974400	Enhancers	Spleen	Spleen
30	chr6:73973400-73974600	Enhancers	Esophagus	oesophagus
31	chr6:73973400-73974800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:73973400-73985000	Weak transcription	Small Intestine	intestine
33	chr6:73973400-73986400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:73973400-74000400	Weak transcription	Aorta	Aorta
35	chr6:73973600-73974000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:73973600-73974000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:73973600-73974000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:73973600-73974000	Enhancers	Lung	lung
39	chr6:73973600-73974000	Active TSS	HSMM	muscle
40	chr6:73973600-73974000	Active TSS	NHLF	lung
41	chr6:73973600-73974200	Enhancers	Brain Substantia Nigra	brain
42	chr6:73973600-73974200	Enhancers	Colon Smooth Muscle	Colon
43	chr6:73973600-73974400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:73973600-73974400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:73973600-73974400	Enhancers	Primary B cells from cord blood	blood
46	chr6:73973600-73974400	Enhancers	Primary hematopoietic stem cells	blood
47	chr6:73973600-73974400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr6:73973600-73974400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:73973600-73974400	Enhancers	Ovary	ovary
50	chr6:73973600-73974400	Enhancers	HUVEC	blood vessel

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