Variant report

Variant	rs3791212
Chromosome Location	chr2:99982201-99982202
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99954615..99957743-chr2:99980170..99982447,3	MCF-7	breast:
2	chr2:99977638..99980361-chr2:99981242..99982894,2	K562	blood:

Variant related genes	Relation type
ENSG00000115514	Chromatin interaction

Extended variants
information (count: 148 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs1011633	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs10172068	0.85[JPT][hapmap]
rs10172752	0.84[JPT][hapmap]
rs10187843	0.84[JPT][hapmap]
rs1053544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10865031	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11123775	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11123782	0.85[JPT][hapmap]
rs11123785	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs11123786	0.85[JPT][hapmap]
rs11676581	0.84[JPT][hapmap]
rs11679115	0.85[ASN][1000 genomes]
rs11683651	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs11686535	0.85[JPT][hapmap]
rs11687870	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs11884686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11887574	0.84[JPT][hapmap]
rs11892441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11899745	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11902994	0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs12052986	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12053519	0.89[JPT][hapmap]
rs12233086	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs12233126	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs12464535	0.85[ASN][1000 genomes]
rs12464785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12465846	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12475639	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12623540	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs13014360	0.83[JPT][hapmap]
rs13017871	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs13018274	0.85[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs13026997	0.85[JPT][hapmap]
rs1376443	0.85[ASN][1000 genomes]
rs1451243	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs1451245	0.89[JPT][hapmap]
rs1451246	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1584647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1584648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17022433	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs17022564	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17022629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1807985	0.87[ASN][1000 genomes]
rs1839666	0.84[EUR][1000 genomes]
rs1839667	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1973011	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2053917	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2122748	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2200578	0.89[JPT][hapmap]
rs2242036	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2290255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2290256	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2290257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2290261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2309576	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2309585	0.85[JPT][hapmap]
rs2309604	0.84[EUR][1000 genomes]
rs2309617	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28382892	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs28382946	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28382984	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3087386	0.84[JPT][hapmap]
rs3749087	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3792134	0.85[JPT][hapmap]
rs3792135	0.87[JPT][hapmap]
rs3792136	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs3792137	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3792142	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3792144	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3792146	0.84[JPT][hapmap]
rs3792149	0.85[JPT][hapmap]
rs3811555	0.85[JPT][hapmap]
rs3828316	0.85[JPT][hapmap]
rs4143760	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4476396	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4535093	0.85[JPT][hapmap]
rs4850901	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4850903	0.85[ASN][1000 genomes]
rs4851200	0.84[JPT][hapmap]
rs4851204	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851205	0.85[JPT][hapmap]
rs4851206	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4851208	0.82[EUR][1000 genomes]
rs55815229	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57242893	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57977991	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58086269	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58958283	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59178618	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59661148	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60257640	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61103312	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62153855	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62155809	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6542879	0.85[JPT][hapmap]
rs6542880	0.85[JPT][hapmap]
rs6542881	0.84[EUR][1000 genomes]
rs6542882	0.85[JPT][hapmap]
rs6708861	0.85[JPT][hapmap]
rs6709240	0.81[ASN][1000 genomes]
rs6711073	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6711977	0.84[JPT][hapmap]
rs6713608	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6714244	0.84[JPT][hapmap]
rs6715321	0.96[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs6720885	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6727483	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs6732750	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6737560	0.84[EUR][1000 genomes]
rs6761390	0.82[EUR][1000 genomes]
rs717454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7558062	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7558074	0.85[ASN][1000 genomes]
rs7560996	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7561079	0.85[JPT][hapmap]
rs7561616	0.85[JPT][hapmap]
rs7563455	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7563462	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7564587	0.84[EUR][1000 genomes]
rs7567674	0.84[JPT][hapmap]
rs7571202	0.85[JPT][hapmap]
rs7572779	0.86[EUR][1000 genomes]
rs7574135	0.85[JPT][hapmap]
rs7579403	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7580448	0.85[JPT][hapmap]
rs7584127	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7585019	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7585721	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs7587419	0.85[JPT][hapmap]
rs7589365	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7591212	0.85[ASN][1000 genomes]
rs7593274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7594838	0.84[JPT][hapmap]
rs7597045	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7597141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7601470	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs7601730	0.85[JPT][hapmap]
rs7602923	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7606977	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs769105	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs896248	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs896249	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs959929	0.85[JPT][hapmap]
rs9941566	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv1014604	chr2:99980851-100097884	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3791212	REV1	Cis_1M	lymphoblastoid	RTeQTL
rs3791212	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs3791212	LYG1	cis	Adipose Subcutaneous	GTEx
rs3791212	LYG1	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99955200-99982600	Weak transcription	Fetal Brain Male	brain
2	chr2:99956200-100004800	Weak transcription	Fetal Heart	heart
3	chr2:99957600-99989400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:99973400-99982600	Weak transcription	Psoas Muscle	Psoas
5	chr2:99974800-99984000	Weak transcription	Pancreas	Pancrea
6	chr2:99975400-100006400	Weak transcription	Stomach Mucosa	stomach
7	chr2:99976000-99989600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:99976200-100003800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:99976200-100004400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:99976400-99988600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:99976400-100003200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr2:99976600-100002400	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr2:99976600-100004800	Strong transcription	Primary B cells from peripheral blood	blood
14	chr2:99976800-99989600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:99977000-99989200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:99977000-99991000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:99977000-99996800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:99977000-100001000	Strong transcription	Primary B cells from cord blood	blood
19	chr2:99977000-100001400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:99977000-100003200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:99977000-100003200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:99977000-100003600	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:99977000-100003800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:99977000-100003800	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:99977200-99989600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:99977200-99991000	Strong transcription	Dnd41	blood
27	chr2:99977200-99996200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:99977600-99997000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:99977600-100002200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:99977600-100003600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:99977800-99989800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:99977800-99989800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr2:99977800-99989800	Strong transcription	Fetal Intestine Large	intestine
34	chr2:99977800-99996800	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:99978000-99989000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:99978200-99986600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:99978200-99990600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:99978200-99997200	Strong transcription	Placenta	Placenta
39	chr2:99978200-100011800	Weak transcription	Esophagus	oesophagus
40	chr2:99978400-99984400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:99978400-99989600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:99978400-99989600	Weak transcription	Spleen	Spleen
43	chr2:99978600-99995600	Weak transcription	Small Intestine	intestine
44	chr2:99979200-99987400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:99979200-99990600	Strong transcription	Left Ventricle	heart
46	chr2:99979400-99982600	Strong transcription	GM12878-XiMat	blood
47	chr2:99979400-99983400	Strong transcription	Ovary	ovary
48	chr2:99979400-99985800	Strong transcription	HepG2	liver
49	chr2:99979400-99986000	Strong transcription	NHDF-Ad	bronchial
50	chr2:99979400-99986200	Strong transcription	K562	blood

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