Variant report

Variant	rs6721031
Chromosome Location	chr2:99941336-99941337
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	chr2:99940620..99944979-chr2:99951072..99952977,3	MCF-7	breast:
2	chr2:99939367..99941723-chr2:99951245..99954484,3	K562	blood:

Variant related genes	Relation type
ENSG00000115514	Chromatin interaction
ENSG00000158417	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10173883	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175852	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176205	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179343	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179435	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179697	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180138	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180688	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182492	0.82[EUR][1000 genomes]
rs10186223	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191001	0.88[ASN][1000 genomes]
rs10207435	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210257	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210346	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10469848	0.82[EUR][1000 genomes]
rs10496337	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123776	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123778	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123783	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12162367	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12617324	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12623835	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989521	0.92[EUR][1000 genomes]
rs12991982	0.84[AFR][1000 genomes]
rs12992356	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13001438	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13017843	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13028722	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032885	0.84[EUR][1000 genomes]
rs13384665	0.94[ASN][1000 genomes]
rs13394927	0.82[EUR][1000 genomes]
rs13401163	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13402784	0.82[EUR][1000 genomes]
rs13405400	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409359	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13415713	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416265	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419448	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420087	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420293	0.82[EUR][1000 genomes]
rs13426758	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13427424	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429185	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429806	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13430662	0.81[ASN][1000 genomes]
rs13430962	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432046	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565054	0.80[EUR][1000 genomes]
rs17022653	0.82[EUR][1000 genomes]
rs17022663	0.82[EUR][1000 genomes]
rs1882598	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1922625	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1922626	0.87[EUR][1000 genomes]
rs1922627	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1948101	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2309577	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309615	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2309616	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28369949	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382945	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382947	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382955	0.82[EUR][1000 genomes]
rs28745279	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3087399	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792151	0.82[EUR][1000 genomes]
rs3828162	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4522654	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4850902	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851197	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4851199	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4851201	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851202	0.85[EUR][1000 genomes]
rs62153853	0.88[AFR][1000 genomes]
rs6542877	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6706425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6712137	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726711	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744199	0.87[EUR][1000 genomes]
rs6745645	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749029	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72815074	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567230	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7567462	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7569805	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579143	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579171	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579999	0.80[EUR][1000 genomes]
rs7581337	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7582085	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582133	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584022	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584705	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7585532	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7599384	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599843	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7603388	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7606279	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9308819	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9308821	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308822	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308823	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9973846	0.86[EUR][1000 genomes];0.87[ASN][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	nsv979073	chr2:99927377-99947554	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6721031	LYG1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99915000-99942800	Weak transcription	Aorta	Aorta
2	chr2:99917200-99948200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:99921000-99942000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:99928200-99951800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:99932000-99951400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:99933000-99949800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:99933000-99950000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:99933400-99945800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:99933400-99946800	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr2:99933400-99949000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:99933400-99949600	Strong transcription	Fetal Muscle Leg	muscle
12	chr2:99933400-99949600	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:99933400-99949800	Strong transcription	Duodenum Mucosa	Duodenum
14	chr2:99933400-99950400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:99933400-99950600	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr2:99933400-99950600	Strong transcription	Fetal Thymus	thymus
17	chr2:99933600-99949000	Strong transcription	Thymus	Thymus
18	chr2:99933600-99949400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:99933600-99949600	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr2:99933600-99949600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:99933600-99949600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:99933600-99949600	Strong transcription	Liver	Liver
23	chr2:99933600-99949600	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:99933600-99949800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:99933600-99949800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:99933600-99949800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:99933600-99949800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:99933600-99949800	Strong transcription	Adipose Nuclei	Adipose
29	chr2:99933600-99949800	Strong transcription	Fetal Muscle Trunk	muscle
30	chr2:99933600-99949800	Strong transcription	Dnd41	blood
31	chr2:99933600-99949800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr2:99933600-99950000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:99933600-99950000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr2:99933600-99950000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:99933600-99950000	Strong transcription	GM12878-XiMat	blood
36	chr2:99933600-99950200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:99933600-99950400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:99933600-99950400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:99933600-99950400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr2:99933600-99950400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:99933600-99950800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:99933800-99945000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr2:99933800-99948800	Strong transcription	HepG2	liver
44	chr2:99933800-99949800	Strong transcription	Fetal Intestine Large	intestine
45	chr2:99933800-99950000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:99933800-99950000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:99933800-99950400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr2:99933800-99950400	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr2:99934000-99947200	Strong transcription	Lung	lung
50	chr2:99934000-99948800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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