Variant report

Variant	rs6709240
Chromosome Location	chr2:99947538-99947539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99945014..99949225-chr2:99950035..99954681,7	K562	blood:
2	chr2:99905599..99909122-chr2:99945751..99948599,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115514	Chromatin interaction
ENSG00000158417	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1000409	0.85[EUR][1000 genomes]
rs10170425	0.83[EUR][1000 genomes]
rs10172068	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10172752	0.85[EUR][1000 genomes]
rs10187843	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10779902	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11123777	0.80[ASN][1000 genomes]
rs11123779	0.80[ASN][1000 genomes]
rs11123782	0.84[ASN][1000 genomes]
rs11123786	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11674219	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11676581	0.80[ASN][1000 genomes]
rs11679115	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11683651	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11685870	0.80[ASN][1000 genomes]
rs11686535	0.84[ASN][1000 genomes]
rs11687870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884686	0.81[ASN][1000 genomes]
rs11887109	0.86[EUR][1000 genomes]
rs11887574	0.82[EUR][1000 genomes]
rs11892472	0.83[ASN][1000 genomes]
rs11897443	0.81[ASN][1000 genomes]
rs11902994	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12464535	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12464785	0.87[ASN][1000 genomes]
rs12475639	0.86[ASN][1000 genomes]
rs12618779	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12621141	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12623540	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13008948	0.84[ASN][1000 genomes]
rs13009884	0.81[ASN][1000 genomes]
rs13010416	0.80[ASN][1000 genomes]
rs13017871	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13018274	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13019192	0.83[ASN][1000 genomes]
rs13026997	0.84[ASN][1000 genomes]
rs13028869	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13033740	0.81[ASN][1000 genomes]
rs13389623	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13392042	0.85[EUR][1000 genomes]
rs13427780	0.83[EUR][1000 genomes]
rs1376443	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1451243	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17022564	0.87[ASN][1000 genomes]
rs1807985	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1825770	0.80[ASN][1000 genomes]
rs1901283	0.83[EUR][1000 genomes]
rs2141908	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2242037	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2290256	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2305354	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2309576	0.81[ASN][1000 genomes]
rs2309585	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2309617	0.81[ASN][1000 genomes]
rs28369943	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28382954	0.82[EUR][1000 genomes]
rs3087386	0.85[EUR][1000 genomes]
rs3791212	0.81[ASN][1000 genomes]
rs3792134	0.84[EUR][1000 genomes]
rs3792146	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3792149	0.85[EUR][1000 genomes]
rs3792152	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3811555	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3828316	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4535093	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4850899	0.80[ASN][1000 genomes]
rs4850901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4850903	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4851200	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4851204	0.81[ASN][1000 genomes]
rs4851205	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55815229	0.87[ASN][1000 genomes]
rs55867742	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs57242893	0.87[ASN][1000 genomes]
rs58086269	0.88[ASN][1000 genomes]
rs59178618	0.81[ASN][1000 genomes]
rs59661148	0.83[ASN][1000 genomes]
rs60294863	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62153855	0.88[ASN][1000 genomes]
rs6542879	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6542880	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6542882	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6708861	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6711977	0.80[ASN][1000 genomes]
rs6713608	0.81[ASN][1000 genomes]
rs6713792	0.83[EUR][1000 genomes]
rs6714244	0.83[EUR][1000 genomes]
rs6717515	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6734290	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6735381	0.80[ASN][1000 genomes]
rs71413827	0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7558062	0.81[ASN][1000 genomes]
rs7558074	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7561079	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7561616	0.81[ASN][1000 genomes]
rs7567674	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7570978	0.80[ASN][1000 genomes]
rs7571202	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7574135	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7579403	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7580448	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7585721	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7586892	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7587419	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7591212	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7597045	0.81[ASN][1000 genomes]
rs7598629	0.85[EUR][1000 genomes]
rs7601470	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7601730	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7602923	0.81[ASN][1000 genomes]
rs7606977	0.81[ASN][1000 genomes]
rs7609108	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs959929	0.85[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6709240	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs6709240	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs6709240	TSGA10	cis	multi-tissue	Pritchard
rs6709240	REV1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99917200-99948200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:99928200-99951800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:99932000-99951400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:99933000-99949800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:99933000-99950000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:99933400-99949000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:99933400-99949600	Strong transcription	Fetal Muscle Leg	muscle
8	chr2:99933400-99949600	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:99933400-99949800	Strong transcription	Duodenum Mucosa	Duodenum
10	chr2:99933400-99950400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:99933400-99950600	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:99933400-99950600	Strong transcription	Fetal Thymus	thymus
13	chr2:99933600-99949000	Strong transcription	Thymus	Thymus
14	chr2:99933600-99949400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:99933600-99949600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr2:99933600-99949600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:99933600-99949600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:99933600-99949600	Strong transcription	Liver	Liver
19	chr2:99933600-99949600	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:99933600-99949800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:99933600-99949800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:99933600-99949800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:99933600-99949800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:99933600-99949800	Strong transcription	Adipose Nuclei	Adipose
25	chr2:99933600-99949800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr2:99933600-99949800	Strong transcription	Dnd41	blood
27	chr2:99933600-99949800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr2:99933600-99950000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:99933600-99950000	Strong transcription	Primary B cells from peripheral blood	blood
30	chr2:99933600-99950000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:99933600-99950000	Strong transcription	GM12878-XiMat	blood
32	chr2:99933600-99950200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:99933600-99950400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:99933600-99950400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr2:99933600-99950400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:99933600-99950400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:99933600-99950800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr2:99933800-99948800	Strong transcription	HepG2	liver
39	chr2:99933800-99949800	Strong transcription	Fetal Intestine Large	intestine
40	chr2:99933800-99950000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:99933800-99950000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:99933800-99950400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr2:99933800-99950400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr2:99934000-99948800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:99934000-99949600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:99934600-99949800	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr2:99934600-99949800	Strong transcription	Placenta	Placenta
48	chr2:99934800-99950000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr2:99934800-99952000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr2:99935000-99949600	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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