Variant report

Variant	rs55867742
Chromosome Location	chr2:99923725-99923726
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1000409	0.84[AMR][1000 genomes]
rs10170425	0.80[AMR][1000 genomes]
rs10172068	0.84[AMR][1000 genomes]
rs10172752	0.84[AMR][1000 genomes]
rs10173466	0.80[AMR][1000 genomes]
rs10186340	0.80[AMR][1000 genomes]
rs10187843	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10779902	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11123777	0.82[ASN][1000 genomes]
rs11123779	0.82[ASN][1000 genomes]
rs11123782	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11123786	0.86[AMR][1000 genomes]
rs11674219	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11676581	0.82[ASN][1000 genomes]
rs11679115	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11683651	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11685870	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11686535	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11687328	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11687870	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11892472	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11895206	0.83[EUR][1000 genomes]
rs11897443	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11902994	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12464535	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12475639	0.81[ASN][1000 genomes]
rs12478488	0.80[AMR][1000 genomes]
rs12618779	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12621141	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12623540	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13008948	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13009884	0.82[ASN][1000 genomes]
rs13010416	0.82[ASN][1000 genomes]
rs13011240	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13014360	0.81[AFR][1000 genomes]
rs13016182	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13017871	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13018274	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13019192	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13026997	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13028869	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13033740	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs13389623	0.87[AMR][1000 genomes]
rs13392042	0.82[AMR][1000 genomes]
rs1376443	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1451243	0.84[AMR][1000 genomes]
rs1807985	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1825770	0.82[ASN][1000 genomes]
rs1901283	0.81[AMR][1000 genomes]
rs2141908	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2242037	0.84[AMR][1000 genomes]
rs2290256	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2305354	0.86[AMR][1000 genomes]
rs2309585	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs28369943	0.84[AMR][1000 genomes]
rs3087386	0.84[AMR][1000 genomes]
rs3792134	0.84[AMR][1000 genomes]
rs3792146	0.82[AMR][1000 genomes]
rs3792149	0.80[AMR][1000 genomes]
rs3792152	0.82[AMR][1000 genomes]
rs3811555	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3828316	0.82[AMR][1000 genomes]
rs4535093	0.84[AMR][1000 genomes]
rs4850899	0.82[ASN][1000 genomes]
rs4850901	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4850903	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4851200	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4851205	0.84[AMR][1000 genomes]
rs59661148	0.83[ASN][1000 genomes]
rs60294863	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6542879	0.84[AMR][1000 genomes]
rs6542880	0.82[AMR][1000 genomes]
rs6708861	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6709240	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6711977	0.82[ASN][1000 genomes]
rs6717515	0.82[AMR][1000 genomes]
rs6732397	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6734290	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6735381	0.82[ASN][1000 genomes]
rs71413827	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7558074	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7561079	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7561616	0.82[ASN][1000 genomes]
rs7567674	0.84[AMR][1000 genomes]
rs7570978	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7571202	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7574135	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7579403	0.86[AMR][1000 genomes]
rs7580448	0.84[AMR][1000 genomes]
rs7585721	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7586892	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7587419	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7591212	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7598629	0.84[AMR][1000 genomes]
rs7601470	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7601730	0.84[AMR][1000 genomes]
rs7609108	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs959929	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv874698	chr2:99827733-99924918	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	nsv1009872	chr2:99840131-99924543	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv1001194	chr2:99840131-99928323	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv1005118	chr2:99841951-99924543	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv1002169	chr2:99846306-99924543	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv1007566	chr2:99847890-99924543	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv999059	chr2:99847890-99926934	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv1003262	chr2:99858556-99924543	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	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
11	nsv961843	chr2:99916605-99924549	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs55867742	REV1	cis	Thyroid	GTEx
rs55867742	REV1	Cis_1M	lymphoblastoid	RTeQTL
rs55867742	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99879000-99933600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:99892400-99935000	Weak transcription	Brain Angular Gyrus	brain
3	chr2:99894200-99934800	Weak transcription	Gastric	stomach
4	chr2:99895400-99935000	Weak transcription	Pancreas	Pancrea
5	chr2:99895800-99933600	Weak transcription	HSMM	muscle
6	chr2:99895800-99933600	Weak transcription	HSMMtube	muscle
7	chr2:99896800-99933400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:99897000-99933600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:99897200-99933800	Weak transcription	Fetal Intestine Small	intestine
10	chr2:99897400-99933800	Weak transcription	HepG2	liver
11	chr2:99898200-99934000	Weak transcription	Small Intestine	intestine
12	chr2:99898400-99938600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:99898600-99933800	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:99899400-99933800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:99899600-99933000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:99899800-99935000	Weak transcription	Esophagus	oesophagus
17	chr2:99900000-99933600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr2:99900400-99933800	Weak transcription	Colonic Mucosa	Colon
19	chr2:99901200-99933400	Weak transcription	Primary B cells from cord blood	blood
20	chr2:99901200-99936600	Weak transcription	Fetal Brain Male	brain
21	chr2:99901600-99933400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:99901600-99933600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:99901600-99933600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:99901600-99933800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr2:99901600-99933800	Weak transcription	Fetal Intestine Large	intestine
26	chr2:99901600-99941200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:99907800-99933800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr2:99908000-99934200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:99908400-99933600	Weak transcription	A549	lung
30	chr2:99912400-99933600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:99913400-99933600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:99914800-99933800	Weak transcription	Lung	lung
33	chr2:99915000-99933400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:99915000-99933600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:99915000-99933600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:99915000-99942800	Weak transcription	Aorta	Aorta
37	chr2:99915200-99933600	Weak transcription	Thymus	Thymus
38	chr2:99915600-99933600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:99916000-99935000	Weak transcription	Hela-S3	cervix
40	chr2:99916800-99933400	Weak transcription	Fetal Thymus	thymus
41	chr2:99917200-99934200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:99917200-99948200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr2:99919000-99933600	Weak transcription	Brain Germinal Matrix	brain
44	chr2:99919000-99933800	Weak transcription	Spleen	Spleen
45	chr2:99919000-99935000	Weak transcription	Right Ventricle	heart
46	chr2:99919200-99933400	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr2:99919200-99933400	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:99919200-99933600	Weak transcription	Adipose Nuclei	Adipose
49	chr2:99919200-99933600	Weak transcription	Brain Anterior Caudate	brain
50	chr2:99919200-99933600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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