Variant report

Variant	rs4851200
Chromosome Location	chr2:99924918-99924919
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr2:99924892-99925119	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
LYG1	TF binding region

Extended variants
information (count: 104 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1000409	0.81[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1011633	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs10172068	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs10172752	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs10187843	0.85[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap]
rs10207981	0.90[JPT][hapmap]
rs1053544	0.90[CHD][hapmap];0.84[JPT][hapmap]
rs10779902	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11123775	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs11123782	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs11123786	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs11674219	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11676581	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs11683651	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs11686535	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs11687870	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11884686	0.84[JPT][hapmap]
rs11887574	0.85[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs11892441	0.84[JPT][hapmap]
rs11899745	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs11902994	0.85[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap]
rs12464785	0.90[CHD][hapmap];0.84[JPT][hapmap]
rs12615519	0.96[CEU][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs12618779	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12621141	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12623540	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs13008948	0.81[ASN][1000 genomes]
rs13014360	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap]
rs13017871	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13018274	0.85[ASW][hapmap];0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes]
rs13026997	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs13028869	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1451243	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs1584647	0.84[JPT][hapmap]
rs1584648	0.84[JPT][hapmap]
rs17022433	0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs17022629	0.84[JPT][hapmap]
rs1807985	0.91[AMR][1000 genomes]
rs2141908	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2242037	0.85[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap]
rs2290255	0.90[CHD][hapmap];0.84[JPT][hapmap]
rs2290256	0.85[ASW][hapmap];0.95[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.87[YRI][hapmap]
rs2290257	0.84[JPT][hapmap]
rs2290261	0.90[CHD][hapmap];0.84[JPT][hapmap]
rs2305354	0.85[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap]
rs2309585	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs2309617	0.90[CHD][hapmap];0.84[JPT][hapmap]
rs3087386	0.86[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs3749087	0.84[JPT][hapmap]
rs3791212	0.84[JPT][hapmap]
rs3792134	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3792137	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs3792142	0.83[JPT][hapmap]
rs3792146	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap]
rs3792149	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3792152	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.84[YRI][hapmap]
rs3811555	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3828316	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs4143760	0.84[JPT][hapmap]
rs4535093	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs4850901	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4851205	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs4851206	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs55867742	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60294863	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6542879	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs6542880	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs6542882	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs6708861	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6709240	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6711977	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs6714244	0.91[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs6715321	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs6721297	0.95[CHB][hapmap];0.83[YRI][hapmap]
rs6722617	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs6734290	0.85[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs71413827	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs717454	0.90[CHD][hapmap];0.84[JPT][hapmap]
rs7561079	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs7561616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7563462	0.84[JPT][hapmap]
rs7567674	0.86[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs7571202	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7574135	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs7579403	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs7580448	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs7585019	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs7585721	0.84[ASW][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap]
rs7587419	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs7593274	0.84[JPT][hapmap]
rs7594838	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs7597141	0.84[JPT][hapmap]
rs7601470	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs7601730	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs7609108	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs769105	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs896248	0.82[JPT][hapmap]
rs896249	0.84[JPT][hapmap]
rs959929	0.91[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4851200	ANKRD23	cis	parietal	SCAN
rs4851200	FAHD2A	cis	cerebellum	SCAN
rs4851200	LIPT1	cis	parietal	SCAN
rs4851200	REV1	cis	Thyroid	GTEx
rs4851200	IL1R2	cis	cerebellum	SCAN
rs4851200	ANKRD36	cis	parietal	SCAN
rs4851200	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs4851200	LIPT1	cis	cerebellum	SCAN
rs4851200	REV1	Cis_1M	lymphoblastoid	RTeQTL
rs4851200	TSGA10	cis	cerebellum	SCAN

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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