Variant report

Variant	rs801201
Chromosome Location	chr7:66024865-66024866
allele	A/G
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	chr7:66024530-66025117	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000177418	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10215132	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10229345	0.89[EUR][1000 genomes]
rs10249404	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10255377	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10263935	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10272357	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10272546	0.81[EUR][1000 genomes]
rs10278371	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10278816	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10281080	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10950044	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11765356	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12533585	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12698534	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13224319	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1860468	0.80[EUR][1000 genomes]
rs1860470	0.82[EUR][1000 genomes]
rs1968127	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2013222	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2191268	0.80[EUR][1000 genomes]
rs2302918	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28698552	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35526611	0.82[EUR][1000 genomes]
rs35986979	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3764903	0.82[EUR][1000 genomes]
rs3857686	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3898855	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4718361	0.87[EUR][1000 genomes]
rs56229325	0.82[AMR][1000 genomes]
rs62465434	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62467857	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6460305	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6460308	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6943696	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6960778	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6965056	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71563125	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7357230	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7807930	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7807944	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs801190	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs801193	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs801196	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs801205	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs801211	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs801216	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs801217	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs810400	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9791890	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv482441	chr7:65885824-66061788	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv3447484	chr7:65909457-66033145	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	esv3377926	chr7:65934493-66051484	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv888327	chr7:65938980-66029429	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
10	esv3423847	chr7:65941210-66054107	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs801201	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs801201	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs801201	RP4-756H11.3	cis	Artery Aorta	GTEx
rs801201	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs801201	RP4-756H11.3	cis	Artery Tibial	GTEx
rs801201	RP4-756H11.3	cis	Whole Blood	GTEx
rs801201	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs801201	RP4-756H11.3	cis	lung	GTEx
rs801201	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs801201	RP4-756H11.3	cis	Thyroid	GTEx
rs801201	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs801201	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs801201	RP4-756H11.3	cis	Stomach	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66004400-66052600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:66004800-66037200	Weak transcription	Psoas Muscle	Psoas
3	chr7:66008600-66056000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr7:66009000-66031400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:66009200-66029400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:66011000-66037000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:66011600-66045000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:66013000-66031800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr7:66018400-66029000	Weak transcription	Primary B cells from cord blood	blood
10	chr7:66019800-66025000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:66019800-66036600	Weak transcription	HUVEC	blood vessel
12	chr7:66019800-66037400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:66020000-66025800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr7:66020000-66025800	Weak transcription	HSMMtube	muscle
15	chr7:66020000-66029000	Weak transcription	HSMM	muscle
16	chr7:66020000-66030400	Weak transcription	Fetal Kidney	kidney
17	chr7:66020000-66031200	Weak transcription	Hela-S3	cervix
18	chr7:66020000-66036600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr7:66020000-66037400	Weak transcription	Small Intestine	intestine
20	chr7:66020600-66030600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:66020600-66031200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr7:66021000-66026400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr7:66021200-66031200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr7:66021800-66025200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr7:66021800-66056400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr7:66022000-66039000	Weak transcription	Aorta	Aorta
27	chr7:66022400-66030600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr7:66022600-66029000	Weak transcription	NHEK	skin
29	chr7:66022600-66031400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr7:66022600-66035200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr7:66022800-66025200	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr7:66023000-66025200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:66023000-66025600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr7:66023000-66026400	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr7:66023000-66026400	Strong transcription	Fetal Intestine Large	intestine
36	chr7:66023000-66030400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr7:66023000-66031200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr7:66023000-66034600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:66023000-66036400	Weak transcription	Brain Substantia Nigra	brain
40	chr7:66023000-66036600	Weak transcription	Brain Anterior Caudate	brain
41	chr7:66023000-66036600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr7:66023000-66037400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr7:66023000-66040800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr7:66023000-66041800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr7:66023200-66025600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr7:66023200-66025600	Strong transcription	Fetal Muscle Trunk	muscle
47	chr7:66023200-66026000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr7:66023200-66026000	Strong transcription	Placenta	Placenta
49	chr7:66023200-66027400	Strong transcription	Fetal Stomach	stomach
50	chr7:66023200-66031000	Weak transcription	Left Ventricle	heart

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