Variant report

Variant	rs28369943
Chromosome Location	chr2:100081323-100081324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100080735..100084657-chr2:100090928..100093443,3	K562	blood:
2	chr2:100079371..100082089-chr2:100106220..100108086,2	MCF-7	breast:
3	chr2:100072001..100074970-chr2:100080545..100083472,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135945	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1000409	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011633	0.84[ASN][1000 genomes]
rs10170425	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10172068	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10172752	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173466	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10186340	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10187843	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10205985	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10779902	0.84[AFR][1000 genomes]
rs10865031	0.88[ASN][1000 genomes]
rs11123786	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11674219	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11679115	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11683651	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11687870	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11887109	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11887574	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11899745	0.88[ASN][1000 genomes]
rs11902994	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12464535	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12465846	0.88[ASN][1000 genomes]
rs12478488	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12618779	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12621141	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12623540	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13017871	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13018274	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13028869	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13384883	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13389623	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13392042	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13394688	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13427780	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1376443	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1451243	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1451246	0.88[ASN][1000 genomes]
rs1807985	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1839666	0.85[ASN][1000 genomes]
rs1839667	0.87[ASN][1000 genomes]
rs1901283	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1973011	0.85[ASN][1000 genomes]
rs2053917	0.88[ASN][1000 genomes]
rs2122748	0.88[ASN][1000 genomes]
rs2141908	0.83[AFR][1000 genomes]
rs2242037	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2290256	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2305354	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2309585	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309586	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2309604	0.84[ASN][1000 genomes]
rs28382954	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3087386	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792134	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792137	0.88[ASN][1000 genomes]
rs3792142	0.87[ASN][1000 genomes]
rs3792144	0.88[ASN][1000 genomes]
rs3792146	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792149	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792152	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3811555	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3828316	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4143760	0.84[ASN][1000 genomes]
rs4476396	0.88[ASN][1000 genomes]
rs4535093	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4850901	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4850903	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4851205	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4851206	0.88[ASN][1000 genomes]
rs4851208	0.85[ASN][1000 genomes]
rs55867742	0.84[AMR][1000 genomes]
rs57977991	0.86[ASN][1000 genomes]
rs60257640	0.88[ASN][1000 genomes]
rs60294863	0.81[AFR][1000 genomes]
rs60335031	0.81[ASN][1000 genomes]
rs62155809	0.87[ASN][1000 genomes]
rs6542879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542880	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6542881	0.82[ASN][1000 genomes]
rs6542882	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6706607	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6708861	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6709240	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6713792	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6714244	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6717515	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6734290	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6737560	0.84[ASN][1000 genomes]
rs71413827	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7558074	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7560795	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7561079	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7563455	0.88[ASN][1000 genomes]
rs7563462	0.88[ASN][1000 genomes]
rs7564587	0.83[ASN][1000 genomes]
rs7567674	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571202	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7572779	0.87[ASN][1000 genomes]
rs7574135	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7579403	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7580448	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7585019	0.88[ASN][1000 genomes]
rs7585721	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7586892	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7587419	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7591212	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7598629	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601470	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7601730	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7609108	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs769105	0.88[ASN][1000 genomes]
rs896248	0.88[ASN][1000 genomes]
rs896249	0.84[ASN][1000 genomes]
rs959929	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	nsv1006625	chr2:99984550-100096371	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers 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
4	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv874700	chr2:100062163-100099989	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv535841	chr2:100072790-100112121	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers 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	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28369943	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs28369943	REV1	Cis_1M	lymphoblastoid	RTeQTL
rs28369943	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs28369943	TSGA10	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100034200-100088800	Weak transcription	Small Intestine	intestine
2	chr2:100041600-100083400	Weak transcription	Brain Substantia Nigra	brain
3	chr2:100048200-100090600	Weak transcription	Stomach Mucosa	stomach
4	chr2:100055400-100083200	Weak transcription	Right Ventricle	heart
5	chr2:100055800-100089000	Weak transcription	Pancreas	Pancrea
6	chr2:100055800-100092600	Weak transcription	Gastric	stomach
7	chr2:100056600-100091000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:100065400-100087400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:100067400-100081400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:100073400-100090000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr2:100074200-100084800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:100075200-100090400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:100075200-100103000	Weak transcription	Hela-S3	cervix
14	chr2:100076200-100098400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:100076200-100105000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:100076400-100084800	Weak transcription	Esophagus	oesophagus
17	chr2:100076600-100085400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:100076600-100094800	Weak transcription	Spleen	Spleen
19	chr2:100076600-100104200	Weak transcription	NHLF	lung
20	chr2:100078400-100083200	Weak transcription	Fetal Heart	heart
21	chr2:100078400-100083400	Weak transcription	Brain Anterior Caudate	brain
22	chr2:100078400-100084800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:100078600-100081600	Weak transcription	Thymus	Thymus
24	chr2:100078600-100084000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr2:100078600-100084800	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:100078600-100085000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr2:100078600-100085200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr2:100078600-100085800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:100078600-100087400	Weak transcription	HMEC	breast
30	chr2:100078600-100087600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:100078600-100088600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:100078600-100088800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr2:100078600-100091000	Weak transcription	Aorta	Aorta
34	chr2:100078600-100091000	Weak transcription	Lung	lung
35	chr2:100078600-100092200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:100078600-100092600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:100078600-100096800	Weak transcription	NH-A	brain
38	chr2:100078800-100082800	Weak transcription	Psoas Muscle	Psoas
39	chr2:100078800-100084800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:100078800-100084800	Weak transcription	Brain Angular Gyrus	brain
41	chr2:100078800-100084800	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:100078800-100084800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr2:100078800-100085000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:100078800-100085000	Weak transcription	Fetal Brain Male	brain
45	chr2:100078800-100085200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr2:100078800-100088800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr2:100078800-100089000	Weak transcription	Ovary	ovary
48	chr2:100078800-100090000	Weak transcription	HUVEC	blood vessel
49	chr2:100078800-100090200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:100078800-100090600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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