Variant report

Variant	rs6720885
Chromosome Location	chr2:99971289-99971290
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	chr2:99951400..99955824-chr2:99970132..99974887,7	MCF-7	breast:
2	chr2:99970079..99971652-chr2:99974840..99977531,2	K562	blood:

Variant related genes	Relation type
ENSG00000158417	Chromatin interaction
ENSG00000115514	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1011633	0.85[EUR][1000 genomes]
rs1053544	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10865031	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11679115	0.84[ASN][1000 genomes]
rs11683651	0.84[ASN][1000 genomes]
rs11884686	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11892441	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11899745	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11902994	0.84[ASN][1000 genomes]
rs12052986	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12464535	0.84[ASN][1000 genomes]
rs12464785	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12465846	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12475639	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12623540	0.84[ASN][1000 genomes]
rs13018274	0.87[ASN][1000 genomes]
rs1376443	0.84[ASN][1000 genomes]
rs1451246	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1584647	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1584648	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17022564	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17022629	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1807985	0.86[ASN][1000 genomes]
rs1839666	0.83[EUR][1000 genomes]
rs1839667	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1973011	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2053917	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2122748	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2290255	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290256	0.82[ASN][1000 genomes]
rs2290261	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2309576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2309604	0.83[EUR][1000 genomes]
rs2309617	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28382946	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28382984	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3749087	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3791212	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792137	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3792142	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3792144	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4143760	0.83[EUR][1000 genomes]
rs4476396	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4850903	0.84[ASN][1000 genomes]
rs4851204	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851206	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4851208	0.81[EUR][1000 genomes]
rs55815229	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57242893	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57977991	0.82[AMR][1000 genomes]
rs58086269	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58958283	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59178618	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59661148	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60257640	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61103312	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62153855	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62155809	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6542881	0.83[EUR][1000 genomes]
rs6711073	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6713608	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6715321	0.81[EUR][1000 genomes]
rs6732750	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6737560	0.83[EUR][1000 genomes]
rs6761390	0.81[EUR][1000 genomes]
rs717454	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7558062	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7558074	0.84[ASN][1000 genomes]
rs7560996	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7563455	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7563462	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7564587	0.83[EUR][1000 genomes]
rs7572779	0.85[EUR][1000 genomes]
rs7584127	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7585019	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7585721	0.84[ASN][1000 genomes]
rs7589365	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7591212	0.84[ASN][1000 genomes]
rs7593274	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7597045	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7597141	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7601470	0.84[ASN][1000 genomes]
rs7602923	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7606977	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs769105	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs896248	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs896249	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv874699	chr2:99898998-100010044	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv524466	chr2:99952086-100031551	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6720885	REV1	Cis_1M	lymphoblastoid	RTeQTL
rs6720885	LYG1	cis	Nerve Tibial	GTEx
rs6720885	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs6720885	LYG1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99955000-99977000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:99955000-99979200	Weak transcription	Fetal Stomach	stomach
3	chr2:99955000-99979800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:99955200-99974400	Weak transcription	Thymus	Thymus
5	chr2:99955200-99979600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:99955200-99982600	Weak transcription	Fetal Brain Male	brain
7	chr2:99955400-99976800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:99955400-99979600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:99955400-99979600	Weak transcription	NH-A	brain
10	chr2:99955600-99978200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:99955800-99976800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:99956000-99976400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:99956200-99976600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr2:99956200-99977600	Weak transcription	Fetal Thymus	thymus
15	chr2:99956200-100004800	Weak transcription	Fetal Heart	heart
16	chr2:99956400-99979600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr2:99956400-99979600	Weak transcription	HUVEC	blood vessel
18	chr2:99956600-99977200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:99957000-99977200	Weak transcription	Dnd41	blood
20	chr2:99957000-99978000	Weak transcription	Small Intestine	intestine
21	chr2:99957400-99978200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:99957600-99973000	Weak transcription	Psoas Muscle	Psoas
23	chr2:99957600-99974200	Weak transcription	Pancreas	Pancrea
24	chr2:99957600-99989400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:99957800-99978200	Weak transcription	Hela-S3	cervix
26	chr2:99958000-99978800	Weak transcription	Fetal Intestine Small	intestine
27	chr2:99958200-99979600	Weak transcription	A549	lung
28	chr2:99958600-99973200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:99959800-99977000	Weak transcription	HepG2	liver
30	chr2:99959800-99980000	Weak transcription	Lung	lung
31	chr2:99960600-99976200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:99961200-99979400	Weak transcription	Ovary	ovary
33	chr2:99962400-99973200	Weak transcription	Left Ventricle	heart
34	chr2:99962400-99979800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:99962400-99979800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:99962600-99977800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:99963000-99976600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:99965000-99977000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:99965000-99977000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr2:99965200-99977000	Weak transcription	Primary B cells from cord blood	blood
41	chr2:99965200-99978000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:99965600-99979800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr2:99966800-99976400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr2:99967000-99977800	Weak transcription	Primary T cells from cord blood	blood
45	chr2:99967200-99976000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr2:99968000-99972600	Weak transcription	GM12878-XiMat	blood
47	chr2:99968000-99977000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr2:99969200-99973800	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr2:99969400-99981600	Weak transcription	Fetal Brain Female	brain
50	chr2:99970200-99971400	Enhancers	HSMM	muscle

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