Variant report

Variant	rs2420612
Chromosome Location	chr7:66001812-66001813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66000362..66002580-chr7:66007526..66009182,2	MCF-7	breast:
2	chr7:65996716..65999287-chr7:66000647..66003151,2	K562	blood:

Variant related genes	Relation type
ENSG00000229180	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1065265	0.87[EUR][1000 genomes]
rs10950035	0.85[EUR][1000 genomes]
rs10950036	0.85[EUR][1000 genomes]
rs10950040	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10950047	0.84[EUR][1000 genomes]
rs11763224	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11766183	0.85[EUR][1000 genomes]
rs11766583	0.85[EUR][1000 genomes]
rs11770063	0.85[EUR][1000 genomes]
rs12666079	0.85[EUR][1000 genomes]
rs12667394	0.86[ASN][1000 genomes]
rs12670811	0.80[EUR][1000 genomes]
rs12672427	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1267814	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13311962	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1638724	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1638725	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1638728	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1638732	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1638735	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1796212	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1796217	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1796218	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1796219	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1796222	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1796226	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1796227	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1862085	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1922722	0.84[EUR][1000 genomes]
rs2052089	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2173571	0.85[EUR][1000 genomes]
rs2279757	0.87[EUR][1000 genomes]
rs2533282	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2533283	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2533284	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2707851	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28425729	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28817617	0.82[EUR][1000 genomes]
rs35459055	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3735147	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3936065	0.85[EUR][1000 genomes]
rs4718335	0.84[EUR][1000 genomes]
rs4718346	0.87[EUR][1000 genomes]
rs4718348	0.80[ASN][1000 genomes]
rs4718364	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4718385	0.85[EUR][1000 genomes]
rs6460298	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6460311	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66594357	0.84[EUR][1000 genomes]
rs6945896	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6947441	0.85[EUR][1000 genomes]
rs6950988	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6960848	0.88[EUR][1000 genomes]
rs6961853	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6966953	0.85[EUR][1000 genomes]
rs6969224	0.83[EUR][1000 genomes]
rs73146609	0.85[EUR][1000 genomes]
rs73148639	0.84[EUR][1000 genomes]
rs73148689	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73150604	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73152714	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73377549	0.84[EUR][1000 genomes]
rs73377594	0.82[EUR][1000 genomes]
rs7785117	0.84[EUR][1000 genomes]
rs7801332	0.85[EUR][1000 genomes]
rs7810213	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7811204	0.85[EUR][1000 genomes]
rs801199	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs801210	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs801212	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs801213	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs964971	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
11	nsv967444	chr7:65992587-66013934	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2420612	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs2420612	GTF2IRD1P1	cis	Thyroid	GTEx
rs2420612	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs2420612	GS1-124K5.4	cis	Stomach	GTEx
rs2420612	GS1-124K5.11	cis	Thyroid	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65983400-66006000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr7:65985800-66006200	Weak transcription	Pancreas	Pancrea
3	chr7:65987800-66006200	Weak transcription	Gastric	stomach
4	chr7:65988400-66006200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:65988600-66006200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr7:65988600-66009000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:65988600-66009000	Weak transcription	HSMMtube	muscle
8	chr7:65988800-66008200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr7:65989000-66006200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr7:65989000-66007600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr7:65989800-66004200	Weak transcription	Dnd41	blood
12	chr7:65990000-66009000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:65990600-66004000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr7:65990600-66005600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:65991200-66009800	Weak transcription	Small Intestine	intestine
16	chr7:65991400-66006200	Weak transcription	Primary B cells from cord blood	blood
17	chr7:65991400-66006200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr7:65991600-66006200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr7:65991800-66007600	Weak transcription	NH-A	brain
20	chr7:65992000-66005000	Weak transcription	Left Ventricle	heart
21	chr7:65992400-66006200	Weak transcription	Osteobl	bone
22	chr7:65993000-66006200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr7:65993400-66006200	Weak transcription	Colonic Mucosa	Colon
24	chr7:65993600-66006200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr7:65993600-66009000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr7:65993600-66009400	Weak transcription	HSMM	muscle
27	chr7:65993800-66006200	Weak transcription	NHEK	skin
28	chr7:65994000-66006200	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr7:65994000-66008400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr7:65994000-66014400	Weak transcription	Colon Smooth Muscle	Colon
31	chr7:65995000-66006200	Weak transcription	Right Ventricle	heart
32	chr7:65995000-66010000	Weak transcription	Fetal Lung	lung
33	chr7:65995000-66017200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr7:65995200-66009000	Weak transcription	Fetal Thymus	thymus
35	chr7:65995400-66002000	Weak transcription	Brain Substantia Nigra	brain
36	chr7:65995400-66006200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr7:65995400-66006400	Weak transcription	Brain Germinal Matrix	brain
38	chr7:65995400-66009000	Weak transcription	Brain Angular Gyrus	brain
39	chr7:65995600-66002200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr7:65995600-66004000	Weak transcription	Aorta	Aorta
41	chr7:65995600-66004800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr7:65995600-66006200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:65995600-66006200	Weak transcription	Primary T cells from cord blood	blood
44	chr7:65995600-66006200	Weak transcription	Brain Anterior Caudate	brain
45	chr7:65995600-66006200	Weak transcription	Brain Hippocampus Middle	brain
46	chr7:65995600-66006200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr7:65995600-66006200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr7:65995600-66006200	Weak transcription	Esophagus	oesophagus
49	chr7:65995600-66006200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr7:65995600-66006200	Weak transcription	NHLF	lung

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