Variant report

Variant	rs4901562
Chromosome Location	chr14:55901373-55901374
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:55888145..55889967-chr14:55899523..55902153,2	K562	blood:
2	chr14:55888467..55890762-chr14:55899523..55901753,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10134905	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10137395	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10144034	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10144130	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10150596	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10150617	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10483642	0.84[AMR][1000 genomes]
rs10782426	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11627790	0.89[EUR][1000 genomes]
rs11845228	0.93[EUR][1000 genomes]
rs12431542	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12886860	0.80[EUR][1000 genomes]
rs12887653	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12888181	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12888191	0.83[EUR][1000 genomes]
rs12888234	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12888361	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12893964	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1538257	0.87[YRI][hapmap]
rs1572613	0.96[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2152975	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2152976	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2185036	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2341538	0.81[JPT][hapmap]
rs28478984	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34652660	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4243600	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4898865	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4901563	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4901564	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4901565	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4901567	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4901568	0.96[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4901569	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4901570	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56015424	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61976569	0.86[EUR][1000 genomes]
rs61976570	0.93[EUR][1000 genomes]
rs61976571	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6573028	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6573029	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6573031	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6573032	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs713477	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7142204	0.96[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7146080	0.84[EUR][1000 genomes]
rs7146170	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7146269	0.92[EUR][1000 genomes]
rs7146306	0.92[EUR][1000 genomes]
rs7146472	0.93[EUR][1000 genomes]
rs7147415	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7147968	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7148481	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7149317	0.81[JPT][hapmap]
rs7149622	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72717779	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8009706	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8010013	0.86[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8014526	0.86[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8014621	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8019270	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs8020152	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9635231	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv901959	chr14:55853724-55916225	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
3	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv564874	chr14:55879685-56027815	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer 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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4901562	EXOC5	cis	parietal	SCAN
rs4901562	RPL13AP3	cis	parietal	SCAN
rs4901562	WDHD1	cis	parietal	SCAN
rs4901562	FBXO34	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55896800-55901400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr14:55897000-55901400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr14:55897000-55901400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr14:55897000-55901400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr14:55897000-55901400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr14:55897800-55907000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr14:55899600-55902400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr14:55899800-55902200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr14:55900000-55902000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr14:55900200-55901400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr14:55900200-55901400	Enhancers	Fetal Thymus	thymus
12	chr14:55900200-55902000	Enhancers	Dnd41	blood
13	chr14:55900400-55901600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
14	chr14:55900600-55901600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr14:55900600-55901800	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr14:55900800-55901600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr14:55901000-55901400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr14:55901000-55901400	Enhancers	Gastric	stomach
19	chr14:55901000-55901600	Enhancers	Duodenum Mucosa	Duodenum
20	chr14:55901000-55901600	Enhancers	Fetal Intestine Small	intestine
21	chr14:55901000-55901800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr14:55901000-55901800	Enhancers	Fetal Intestine Large	intestine
23	chr14:55901000-55902000	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr14:55901000-55902000	Enhancers	Hela-S3	cervix
25	chr14:55901000-55902600	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr14:55901200-55901600	Flanking Active TSS	HepG2	liver
27	chr14:55901200-55901800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr14:55901200-55901800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr14:55901200-55901800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr14:55901200-55902000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr14:55901200-55902400	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr14:55901200-55902400	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr14:55901200-55902600	Enhancers	Primary T cells from cord blood	blood

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