Variant report

Variant	rs1878109
Chromosome Location	chr2:86982876-86982877
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86975250..86978690-chr2:86981648..86984537,4	K562	blood:
2	chr2:86976811..86978782-chr2:86981681..86983709,3	K562	blood:

Variant related genes	Relation type
ENSG00000153561	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10186663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10201422	0.89[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1049457	0.83[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1049458	0.89[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11547281	0.86[CHD][hapmap]
rs11889231	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1193	0.89[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12613610	0.86[CEU][hapmap]
rs12714203	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12997796	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[ASN][1000 genomes]
rs13004867	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs13297	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1850138	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2063848	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs2138396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2138397	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs2271666	0.83[MEX][hapmap]
rs2367378	0.89[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2367379	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2887012	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34353387	0.86[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs34933869	0.83[ASN][1000 genomes]
rs35129240	0.83[ASN][1000 genomes]
rs35594332	0.86[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs35815787	0.83[ASN][1000 genomes]
rs36100635	0.95[CEU][hapmap];0.89[TSI][hapmap]
rs4832049	0.88[MEX][hapmap]
rs4832311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4832312	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6547705	0.83[MEX][hapmap]
rs6705448	0.83[MEX][hapmap]
rs6706378	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6711696	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6711700	0.81[EUR][1000 genomes]
rs6726451	0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6731890	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561172	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7596943	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309636	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309637	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309638	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs938486	0.90[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv10063	chr2:86940988-87084360	Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1002420	chr2:86948835-87172715	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv874472	chr2:86961252-87071474	Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1008817	chr2:86970406-87172715	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv14382	chr2:86972214-87174121	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv997982	chr2:86972834-87105864	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1007746	chr2:86972834-87172715	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv521780	chr2:86974318-86994719	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv458585	chr2:86974318-87108211	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv582373	chr2:86974318-87108211	Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv1007307	chr2:86974563-87055214	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv535809	chr2:86974563-87055214	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv1003748	chr2:86975514-87032318	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
15	nsv535810	chr2:86975514-87032318	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
16	nsv1004572	chr2:86975514-87082883	Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
17	nsv535811	chr2:86975514-87082883	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1878109	RMND5A	cis	cerebellum	SCAN
rs1878109	PLGLB1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86968600-86993000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:86968600-86997600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:86969200-86986400	Strong transcription	Fetal Thymus	thymus
4	chr2:86969200-86997800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:86969400-86984400	Weak transcription	Fetal Heart	heart
6	chr2:86969400-86997800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:86969600-86995400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:86969600-86995400	Weak transcription	Esophagus	oesophagus
9	chr2:86970000-87002000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:86970400-86995400	Weak transcription	Aorta	Aorta
11	chr2:86971600-86993000	Weak transcription	Lung	lung
12	chr2:86972000-86987600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:86972000-86993000	Weak transcription	Right Ventricle	heart
14	chr2:86972000-86993000	Weak transcription	Spleen	Spleen
15	chr2:86972000-86995400	Weak transcription	Pancreas	Pancrea
16	chr2:86974200-87004200	Weak transcription	Small Intestine	intestine
17	chr2:86974600-86987600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:86974800-86999800	Weak transcription	Stomach Mucosa	stomach
19	chr2:86975200-86986600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:86975200-86992600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr2:86975400-86993000	Weak transcription	Gastric	stomach
22	chr2:86975400-87003000	Weak transcription	Fetal Brain Male	brain
23	chr2:86975800-86999600	Weak transcription	NHLF	lung
24	chr2:86975800-87006600	Weak transcription	NH-A	brain
25	chr2:86976400-86985000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:86976800-86983200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:86976800-86983800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr2:86977200-86984200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:86977400-86984000	Strong transcription	Liver	Liver
30	chr2:86977400-86986000	Strong transcription	Dnd41	blood
31	chr2:86977600-86983400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:86977600-86985200	Strong transcription	Primary T cells from cord blood	blood
33	chr2:86977600-86997800	Weak transcription	HSMMtube	muscle
34	chr2:86977800-86983000	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr2:86977800-86983800	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr2:86977800-86983800	Strong transcription	Primary B cells from peripheral blood	blood
37	chr2:86977800-86984800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr2:86977800-86985200	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr2:86977800-86995400	Weak transcription	Fetal Brain Female	brain
40	chr2:86978000-86983600	Strong transcription	Hela-S3	cervix
41	chr2:86978000-86984000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr2:86978000-86985200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr2:86978000-86985200	Strong transcription	Fetal Intestine Large	intestine
44	chr2:86978000-86985200	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr2:86978000-86985400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr2:86978200-86984600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:86978200-86985200	Strong transcription	Thymus	Thymus
48	chr2:86978200-87003000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr2:86978400-86984000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr2:86978400-86988600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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