Variant report

Variant	rs13235972
Chromosome Location	chr7:65883605-65883606
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65883342..65885177-chr7:65887474..65889695,2	K562	blood:

Variant related genes	Relation type
ENSG00000231234	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10247526	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10807701	0.88[EUR][1000 genomes]
rs10807702	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10950032	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12530490	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1267816	1.00[AFR][1000 genomes]
rs1267819	1.00[AFR][1000 genomes]
rs1267820	1.00[AFR][1000 genomes]
rs13222887	1.00[AFR][1000 genomes]
rs13224048	1.00[AFR][1000 genomes]
rs13232193	0.87[AFR][1000 genomes]
rs13237037	1.00[AFR][1000 genomes]
rs13237344	0.95[AFR][1000 genomes]
rs13241548	1.00[AFR][1000 genomes]
rs13242216	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1392104	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1499613	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1499614	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1532573	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1553174	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1618893	1.00[AFR][1000 genomes]
rs1638734	1.00[AFR][1000 genomes]
rs1796215	1.00[AFR][1000 genomes]
rs1796220	1.00[AFR][1000 genomes]
rs1796228	1.00[AFR][1000 genomes]
rs1979823	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2533288	0.95[AFR][1000 genomes]
rs2707831	1.00[AFR][1000 genomes]
rs2707844	0.95[AFR][1000 genomes]
rs34192067	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34363376	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34700450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34807232	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35261784	0.82[AFR][1000 genomes]
rs35823062	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35825036	0.90[AFR][1000 genomes]
rs36104268	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4149468	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4481472	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4718317	0.86[AFR][1000 genomes]
rs4718333	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58668827	1.00[AFR][1000 genomes]
rs58669269	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66630579	0.85[AFR][1000 genomes]
rs6958289	0.86[AFR][1000 genomes]
rs6958420	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6964245	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6964530	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs71563118	0.95[AFR][1000 genomes]
rs7778911	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs778679	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778683	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778687	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778691	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs778693	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs778698	0.86[ASN][1000 genomes]
rs778701	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs778704	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs778717	0.82[ASN][1000 genomes]
rs778729	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778732	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778733	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7792391	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7804223	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7808834	0.83[AFR][1000 genomes];0.82[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	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv981507	chr7:65878773-65886496	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13235972	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs13235972	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs13235972	ASL	cis	multi-tissue	Pritchard
rs13235972	RP4-756H11.3	cis	lung	GTEx
rs13235972	VKORC1L1	cis	Whole Blood	GTEx
rs13235972	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs13235972	GUSB	cis	Whole Blood	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65875200-65884400	Weak transcription	K562	blood
2	chr7:65876200-65888600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:65877000-65888600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:65879000-65890000	Weak transcription	HSMM	muscle
5	chr7:65879000-65891800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:65879000-65893200	Weak transcription	Aorta	Aorta
7	chr7:65879000-65905600	Weak transcription	Lung	lung
8	chr7:65879000-65909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:65879000-65922200	Weak transcription	Small Intestine	intestine
10	chr7:65879200-65886800	Weak transcription	Brain Hippocampus Middle	brain
11	chr7:65879200-65888600	Weak transcription	Adipose Nuclei	Adipose
12	chr7:65879200-65889600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr7:65879200-65891400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr7:65879200-65893000	Weak transcription	Gastric	stomach
15	chr7:65879200-65893800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr7:65879200-65894600	Weak transcription	HMEC	breast
17	chr7:65879200-65894800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:65879200-65896000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr7:65879200-65902000	Weak transcription	Brain Substantia Nigra	brain
20	chr7:65879200-65904000	Weak transcription	Fetal Lung	lung
21	chr7:65879200-65907400	Weak transcription	Esophagus	oesophagus
22	chr7:65879200-65924600	Weak transcription	Brain Anterior Caudate	brain
23	chr7:65879200-65939800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr7:65879200-65946000	Weak transcription	NHEK	skin
25	chr7:65879200-65957600	Weak transcription	Psoas Muscle	Psoas
26	chr7:65879400-65884600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:65879400-65888200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr7:65879400-65889400	Weak transcription	Fetal Muscle Leg	muscle
29	chr7:65879400-65889600	Weak transcription	Primary T cells from cord blood	blood
30	chr7:65879400-65889800	Weak transcription	Ovary	ovary
31	chr7:65879400-65890800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr7:65879400-65891200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr7:65879400-65891400	Weak transcription	Colonic Mucosa	Colon
34	chr7:65879400-65892600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr7:65879400-65900600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr7:65879400-65901000	Weak transcription	Brain Angular Gyrus	brain
37	chr7:65879400-65901200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr7:65879400-65909200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr7:65879400-65914200	Weak transcription	Left Ventricle	heart
40	chr7:65879400-65914200	Weak transcription	GM12878-XiMat	blood
41	chr7:65879400-65917200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr7:65879400-65921000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr7:65879400-65921400	Weak transcription	Fetal Kidney	kidney
44	chr7:65879600-65888600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr7:65879600-65888800	Weak transcription	Fetal Intestine Small	intestine
46	chr7:65879600-65889600	Weak transcription	Fetal Intestine Large	intestine
47	chr7:65879600-65892200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr7:65879600-65893800	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr7:65879600-65895000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr7:65879600-65899400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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