Variant report

Variant	rs28382954
Chromosome Location	chr2:100026542-100026543
allele	C/T
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	POLR2A	chr2:100026469-100027606	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr2:100010038-100028424	K562	blood:	n/a	n/a
3	POLR2A	chr2:100026454-100026554	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:100019322..100022368-chr2:100023817..100027425,5	K562	blood:
2	chr2:100018784..100022368-chr2:100023520..100027749,4	K562	blood:

Variant related genes	Relation type
REV1	TF binding region
ENSG00000273306	Chromatin interaction
ENSG00000135945	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1000409	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10170425	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10172068	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10172752	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10173466	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10186340	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10187843	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10205985	0.86[AMR][1000 genomes]
rs11123786	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11674219	0.81[EUR][1000 genomes]
rs11679115	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11683651	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11687870	0.82[EUR][1000 genomes]
rs11887109	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11887574	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11888134	0.81[EUR][1000 genomes]
rs11902994	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12464535	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12478488	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12618779	0.82[EUR][1000 genomes]
rs12621141	0.82[AMR][1000 genomes]
rs12623540	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13017871	0.81[EUR][1000 genomes]
rs13018274	0.86[EUR][1000 genomes]
rs13028869	0.81[EUR][1000 genomes]
rs13384883	0.88[AMR][1000 genomes]
rs13389623	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13392042	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13394688	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13427780	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1376443	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1451243	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1807985	0.84[EUR][1000 genomes]
rs1901283	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2242037	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2290256	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2305354	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2309585	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2309586	0.84[AMR][1000 genomes]
rs28369943	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3087386	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3792134	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3792146	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3792149	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3792152	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3811555	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3828316	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4535093	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4850901	0.83[EUR][1000 genomes]
rs4850903	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4851205	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6542879	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6542880	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6542882	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6706607	0.84[AMR][1000 genomes]
rs6708861	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6709240	0.82[EUR][1000 genomes]
rs6713792	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6714244	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6717515	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6734290	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7558074	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7560795	0.83[AMR][1000 genomes]
rs7561079	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7567674	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7571202	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7574135	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7579403	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7580448	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7585721	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7586892	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7587419	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7591212	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7598629	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7601470	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7601730	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7609108	0.82[EUR][1000 genomes]
rs959929	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[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	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
3	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
4	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
5	nsv1014161	chr2:100021040-100063406	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28382954	REV1	Cis_1M	lymphoblastoid	RTeQTL
rs28382954	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs28382954	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99999400-100056800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:100004800-100044800	Strong transcription	Primary T helper cells PMA-I stimulated	--
3	chr2:100005200-100049800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:100005600-100045400	Strong transcription	Primary T cells from cord blood	blood
5	chr2:100005800-100045200	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr2:100005800-100062600	Strong transcription	Dnd41	blood
7	chr2:100005800-100066000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:100006000-100034200	Strong transcription	GM12878-XiMat	blood
9	chr2:100006000-100046400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:100006000-100049600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:100006000-100050800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr2:100006000-100051000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:100006000-100081200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr2:100006200-100028600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:100006200-100046400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr2:100006200-100051400	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr2:100006400-100034200	Strong transcription	Fetal Brain Female	brain
18	chr2:100006400-100046600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:100006600-100042600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr2:100007000-100035400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:100009000-100045000	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr2:100009400-100034200	Strong transcription	Stomach Smooth Muscle	stomach
23	chr2:100009800-100050000	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:100014400-100039000	Strong transcription	Adipose Nuclei	Adipose
25	chr2:100015600-100035400	Strong transcription	HSMM	muscle
26	chr2:100019200-100031200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:100020600-100051400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:100020800-100050200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:100021000-100051800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:100021200-100050800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:100021200-100077800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:100021400-100049200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:100021400-100050800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:100021600-100040400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr2:100021800-100029000	Weak transcription	Fetal Brain Male	brain
36	chr2:100022000-100030200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:100022000-100036600	Strong transcription	Placenta	Placenta
38	chr2:100022000-100047600	Weak transcription	Stomach Mucosa	stomach
39	chr2:100022000-100050000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:100022000-100054800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:100022200-100028800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:100022200-100029200	Weak transcription	Psoas Muscle	Psoas
43	chr2:100022200-100031600	Weak transcription	Gastric	stomach
44	chr2:100022200-100034800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:100022200-100059000	Strong transcription	Liver	Liver
46	chr2:100022400-100028400	Weak transcription	Fetal Lung	lung
47	chr2:100022400-100033800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr2:100022400-100039200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:100022600-100026800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:100022600-100030200	Weak transcription	Brain Germinal Matrix	brain

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