Variant report

Variant	rs7599384
Chromosome Location	chr2:99968107-99968108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99954792..99957278-chr2:99966489..99969088,2	MCF-7	breast:
2	chr2:99952025..99954786-chr2:99968103..99970099,2	MCF-7	breast:
3	chr2:99966555..99969131-chr2:100104405..100107106,2	MCF-7	breast:
4	chr2:99961156..99963185-chr2:99963763..99968459,4	K562	blood:

Variant related genes	Relation type
ENSG00000115514	Chromatin interaction
ENSG00000158417	Chromatin interaction
ENSG00000135945	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10173883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175852	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176205	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179343	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179435	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182492	0.90[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs10186223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10207435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10469848	0.82[EUR][1000 genomes]
rs10496337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865030	0.80[CEU][hapmap]
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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12162367	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12617324	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12623835	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989521	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12991982	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12992356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13001438	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13017843	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13028722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032885	0.84[EUR][1000 genomes]
rs13384665	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13394927	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs13401163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13402784	0.89[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs13405400	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13415713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419448	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420087	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420293	0.90[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs13426758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13427424	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13430662	0.81[ASN][1000 genomes]
rs13430962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431410	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap]
rs13432046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565054	0.80[EUR][1000 genomes]
rs17022653	0.90[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs17022663	0.90[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs1882598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1922625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1922626	0.88[CEU][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[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	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382945	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382947	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382955	0.82[EUR][1000 genomes]
rs28745279	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3087399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792151	0.89[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs3828162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4522654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4850902	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851189	0.80[CEU][hapmap]
rs4851191	0.90[CEU][hapmap]
rs4851197	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4851199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4851201	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851202	0.85[EUR][1000 genomes]
rs62153853	0.81[AFR][1000 genomes]
rs6542877	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6706425	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6712137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721031	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744199	0.87[EUR][1000 genomes]
rs6745645	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749029	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72815074	0.88[AFR][1000 genomes];1.00[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579171	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579999	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs7581337	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7582085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584022	0.84[AFR][1000 genomes];0.90[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]
rs7586635	0.82[CEU][hapmap]
rs7599843	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7603388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7606279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9308819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9308821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308823	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9973846	0.85[AMR][1000 genomes];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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7599384	LYG1	cis	Whole Blood	GTEx

Chromatin state (count:66 , 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	chr2:99955400-99970000	Weak transcription	NHDF-Ad	bronchial
8	chr2:99955400-99976800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:99955400-99979600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:99955400-99979600	Weak transcription	NH-A	brain
11	chr2:99955600-99978200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:99955800-99976800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:99956000-99976400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:99956200-99970200	Weak transcription	Osteobl	bone
15	chr2:99956200-99976600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr2:99956200-99977600	Weak transcription	Fetal Thymus	thymus
17	chr2:99956200-100004800	Weak transcription	Fetal Heart	heart
18	chr2:99956400-99979600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:99956400-99979600	Weak transcription	HUVEC	blood vessel
20	chr2:99956600-99977200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:99957000-99977200	Weak transcription	Dnd41	blood
22	chr2:99957000-99978000	Weak transcription	Small Intestine	intestine
23	chr2:99957400-99978200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:99957600-99973000	Weak transcription	Psoas Muscle	Psoas
25	chr2:99957600-99974200	Weak transcription	Pancreas	Pancrea
26	chr2:99957600-99989400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:99957800-99978200	Weak transcription	Hela-S3	cervix
28	chr2:99958000-99969800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:99958000-99970000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:99958000-99978800	Weak transcription	Fetal Intestine Small	intestine
31	chr2:99958200-99970000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:99958200-99970200	Weak transcription	NHEK	skin
33	chr2:99958200-99979600	Weak transcription	A549	lung
34	chr2:99958600-99973200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:99959800-99977000	Weak transcription	HepG2	liver
36	chr2:99959800-99980000	Weak transcription	Lung	lung
37	chr2:99960600-99976200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:99961200-99979400	Weak transcription	Ovary	ovary
39	chr2:99962400-99970600	Weak transcription	HMEC	breast
40	chr2:99962400-99973200	Weak transcription	Left Ventricle	heart
41	chr2:99962400-99979800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:99962400-99979800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:99962600-99977800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:99963000-99976600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:99965000-99977000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:99965000-99977000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr2:99965200-99977000	Weak transcription	Primary B cells from cord blood	blood
48	chr2:99965200-99978000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:99965600-99970000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:99965600-99979800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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