Variant report

Variant	rs2003300
Chromosome Location	chr7:66147746-66147747
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:66145930..66148922-chr7:66213233..66215140,2	MCF-7	breast:
2	chr7:66147345..66148941-chr7:66150960..66153085,3	K562	blood:
3	chr7:66118152..66121117-chr7:66145225..66147766,4	MCF-7	breast:
4	chr7:66145800..66148420-chr7:66309175..66311369,3	MCF-7	breast:
5	chr1:180123619..180124402-chr7:66147119..66147881,2	NB4	blood:
6	chr7:66144717..66148625-chr7:66203954..66207507,5	K562	blood:
7	chr7:66145819..66148736-chr7:66203770..66205462,3	MCF-7	breast:
8	chr7:66119490..66121348-chr7:66145844..66148158,2	K562	blood:
9	chr7:66144687..66148625-chr7:66203954..66207507,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272831	Chromatin interaction
ENSG00000243335	Chromatin interaction
ENSG00000230583	Chromatin interaction
ENSG00000271064	Chromatin interaction
ENSG00000226824	Chromatin interaction
ENSG00000154710	Chromatin interaction
ENSG00000116260	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 17 )

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

rs_ID	r²[population]
rs10107	0.94[YRI][hapmap]
rs1016265	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10233806	0.84[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10244498	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10274883	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10278014	0.94[YRI][hapmap]
rs10281499	0.94[YRI][hapmap]
rs10950049	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10950050	0.81[AFR][1000 genomes]
rs11761542	0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs11772819	0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs12532998	0.83[CEU][hapmap]
rs12673450	0.94[YRI][hapmap]
rs13226966	0.86[AFR][1000 genomes]
rs13242290	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13308803	0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs13536	0.94[YRI][hapmap]
rs1544549	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1860469	0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs1860472	0.83[AFR][1000 genomes]
rs1962050	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2013908	0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2109297	0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2420820	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2659890	0.88[AFR][1000 genomes]
rs2659891	0.91[AFR][1000 genomes]
rs2659892	0.92[AFR][1000 genomes]
rs2659893	0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs2659894	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659895	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659896	0.83[AFR][1000 genomes]
rs2659897	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2659898	0.92[AFR][1000 genomes]
rs2659900	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2659901	0.90[AFR][1000 genomes]
rs2659904	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2659907	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2659908	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2659914	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2707824	0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs2707837	0.90[AFR][1000 genomes]
rs2707839	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2707847	0.92[AFR][1000 genomes]
rs28480509	0.84[AFR][1000 genomes]
rs3735148	0.83[CEU][hapmap]
rs3846973	0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3857687	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4610622	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4717315	0.85[AFR][1000 genomes]
rs4718383	0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs58347342	0.90[AFR][1000 genomes]
rs6460302	0.89[YRI][hapmap]
rs6460304	0.89[YRI][hapmap]
rs6460307	0.94[YRI][hapmap]
rs66981195	0.83[AFR][1000 genomes]
rs6950137	0.94[YRI][hapmap]
rs6951302	0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6955837	0.94[YRI][hapmap]
rs6958200	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6969679	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6975044	0.85[AFR][1000 genomes]
rs6978178	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs721717	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7782587	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7792762	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7800620	0.82[CHB][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs7805152	0.84[AFR][1000 genomes]
rs801195	0.93[YRI][hapmap]
rs801204	0.93[YRI][hapmap]
rs881285	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs974239	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9791712	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9791713	0.94[YRI][hapmap];0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv981398	chr7:66138644-66147890	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv3385090	chr7:66146376-66205022	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS 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
5	esv3401338	chr7:66147493-66206298	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2003300	RP4-756H11.3	cis	lung	GTEx
rs2003300	RP4-756H11.3	cis	Artery Aorta	GTEx
rs2003300	GS1-124K5.4	cis	Stomach	GTEx
rs2003300	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs2003300	GTF2IRD1P1	cis	Thyroid	GTEx
rs2003300	RNU6-96P	cis	Thyroid	GTEx
rs2003300	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs2003300	GS1-124K5.4	cis	Artery Aorta	GTEx
rs2003300	GS1-124K5.11	cis	Thyroid	GTEx
rs2003300	RP4-756H11.3	cis	Thyroid	GTEx
rs2003300	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs2003300	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs2003300	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2003300	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs2003300	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs2003300	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs2003300	RP4-756H11.3	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66146000-66147800	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr7:66146000-66147800	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr7:66146000-66148200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr7:66146000-66148400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr7:66146000-66148400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:66146000-66148400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr7:66146000-66148800	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr7:66146000-66149200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr7:66146200-66147800	Active TSS	Liver	Liver
10	chr7:66146200-66148000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr7:66146200-66148000	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr7:66146200-66148200	Active TSS	H1 Cell Line	embryonic stem cell
13	chr7:66146200-66148200	Active TSS	Psoas Muscle	Psoas
14	chr7:66146200-66148400	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr7:66146200-66148600	Active TSS	Rectal Smooth Muscle	rectum
16	chr7:66146200-66148600	Active TSS	GM12878-XiMat	blood
17	chr7:66146200-66149000	Active TSS	HSMM	muscle
18	chr7:66146400-66147800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:66146400-66147800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:66146400-66147800	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr7:66146400-66147800	Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr7:66146400-66147800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
23	chr7:66146400-66147800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr7:66146400-66147800	Active TSS	Fetal Intestine Large	intestine
25	chr7:66146400-66147800	Active TSS	Fetal Intestine Small	intestine
26	chr7:66146400-66147800	Active TSS	Pancreas	Pancrea
27	chr7:66146400-66147800	Active TSS	Stomach Mucosa	stomach
28	chr7:66146400-66147800	Active TSS	K562	blood
29	chr7:66146400-66148000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr7:66146400-66148000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr7:66146400-66148000	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr7:66146400-66148000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr7:66146400-66148000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr7:66146400-66148000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr7:66146400-66148000	Active TSS	Aorta	Aorta
36	chr7:66146400-66148000	Active TSS	Brain Substantia Nigra	brain
37	chr7:66146400-66148000	Active TSS	Left Ventricle	heart
38	chr7:66146400-66148200	Active TSS	H9 Cell Line	embryonic stem cell
39	chr7:66146400-66148200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr7:66146400-66148200	Active TSS	Fetal Kidney	kidney
41	chr7:66146400-66148200	Active TSS	Gastric	stomach
42	chr7:66146400-66148200	Active TSS	Ovary	ovary
43	chr7:66146400-66148200	Active TSS	A549	lung
44	chr7:66146400-66148400	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr7:66146400-66148400	Active TSS	Esophagus	oesophagus
46	chr7:66146400-66148600	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr7:66146400-66148600	Active TSS	HSMMtube	muscle
48	chr7:66146400-66148800	Active TSS	Muscle Satellite Cultured Cells	--
49	chr7:66146400-66149000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr7:66146400-66149000	Active TSS	NHDF-Ad	bronchial

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