Variant report

Variant	rs6587562
Chromosome Location	chr1:151246241-151246242
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151241271..151243134-chr1:151244958..151246812,2	K562	blood:
2	chr1:151167814..151170369-chr1:151245194..151246986,2	MCF-7	breast:
3	chr1:151245093..151248113-chr1:151249690..151252378,3	MCF-7	breast:
4	chr1:151245378..151247558-chr1:151247994..151250804,2	K562	blood:
5	1:151245172-151246650..1:151516085-151535167	Hela-S3	cervix:
6	chr1:151245277..151246878-chr1:151247994..151250057,2	K562	blood:
7	1:151245172-151246650..1:151411623-151426875	Hela-S3	cervix:
8	chr1:151244636..151246334-chr1:151253644..151256632,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000232671	Chromatin interaction
ENSG00000207606	Chromatin interaction
ENSG00000223861	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000143367	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1056847	0.93[GIH][hapmap];1.00[JPT][hapmap]
rs10749660	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10788801	0.86[JPT][hapmap]
rs10788803	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs10888408	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10888409	0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10888410	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10888411	0.82[ASN][1000 genomes]
rs11204785	0.85[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs11204791	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204795	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12022732	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12040384	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12048670	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12062719	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12080778	0.88[EUR][1000 genomes]
rs12407426	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1536617	0.91[JPT][hapmap]
rs16827941	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16833079	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1752387	0.85[JPT][hapmap]
rs1892196	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2025900	0.82[JPT][hapmap]
rs2031797	0.83[GIH][hapmap];0.91[JPT][hapmap]
rs2275900	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2769268	0.82[JPT][hapmap]
rs2769273	0.82[JPT][hapmap]
rs2800946	0.82[JPT][hapmap]
rs3811405	0.86[JPT][hapmap]
rs3811406	0.85[GIH][hapmap];0.91[JPT][hapmap]
rs41302131	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4246525	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4291501	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4520422	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4522000	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4636463	0.90[JPT][hapmap]
rs4970944	0.81[ASW][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap]
rs4970948	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs4971013	0.94[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4971015	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4971016	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971021	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971023	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971025	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4971026	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4971027	1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4971029	0.91[JPT][hapmap]
rs4971030	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4971032	0.87[ASN][1000 genomes]
rs5022636	0.95[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap]
rs58323986	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61817972	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6587559	0.94[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6678528	0.86[JPT][hapmap]
rs6681071	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6681163	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6683396	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6686402	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6695344	0.90[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs6701325	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7518924	0.87[ASN][1000 genomes]
rs7521064	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7527032	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7532935	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7539584	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7544947	0.94[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7545392	0.95[JPT][hapmap]
rs7552906	0.80[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs943637	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[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	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
2	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
3	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
4	esv2754960	chr1:151240542-151331304	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	esv34461	chr1:151240542-151411635	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	esv2753774	chr1:151240542-151411635	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6587562	SELENBP1	cis	cerebellum	SCAN
rs6587562	LCE5A	cis	cerebellum	SCAN
rs6587562	CTSS	cis	cerebellum	SCAN
rs6587562	HIST2H2AC	cis	parietal	SCAN
rs6587562	PSMD4	cis	parietal	SCAN
rs6587562	PSMD4	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151228400-151253400	Weak transcription	Fetal Brain Male	brain
2	chr1:151234600-151246800	Strong transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:151235000-151253400	Weak transcription	Stomach Mucosa	stomach
4	chr1:151237600-151253200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:151239000-151253200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:151239400-151253400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:151240200-151253400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:151240400-151247800	Weak transcription	Primary B cells from cord blood	blood
9	chr1:151240400-151249000	Weak transcription	GM12878-XiMat	blood
10	chr1:151240400-151253200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:151240400-151253200	Weak transcription	Hela-S3	cervix
12	chr1:151240400-151253400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:151240600-151246400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:151240600-151246600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:151240600-151249000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:151240600-151249200	Weak transcription	Spleen	Spleen
17	chr1:151240600-151250200	Weak transcription	HepG2	liver
18	chr1:151240600-151253200	Weak transcription	Primary T cells from cord blood	blood
19	chr1:151240600-151253200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:151240600-151253200	Weak transcription	Right Ventricle	heart
21	chr1:151240600-151253200	Weak transcription	Dnd41	blood
22	chr1:151240600-151253400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:151240600-151253400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:151240600-151253400	Weak transcription	Brain Substantia Nigra	brain
25	chr1:151240600-151253400	Weak transcription	Colonic Mucosa	Colon
26	chr1:151240600-151253400	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:151240600-151253400	Weak transcription	Esophagus	oesophagus
28	chr1:151240600-151253400	Weak transcription	Fetal Kidney	kidney
29	chr1:151240600-151253400	Weak transcription	Fetal Lung	lung
30	chr1:151240600-151253400	Weak transcription	Pancreas	Pancrea
31	chr1:151240600-151253400	Weak transcription	Psoas Muscle	Psoas
32	chr1:151240600-151253400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:151240600-151253400	Weak transcription	HMEC	breast
34	chr1:151240600-151253400	Weak transcription	NHLF	lung
35	chr1:151240600-151254000	Weak transcription	Aorta	Aorta
36	chr1:151240800-151246600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:151240800-151247400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:151240800-151249200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:151240800-151253400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:151240800-151253400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:151240800-151253400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:151240800-151253400	Weak transcription	Fetal Intestine Large	intestine
43	chr1:151240800-151253400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:151240800-151253600	Weak transcription	Small Intestine	intestine
45	chr1:151241200-151247600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:151241600-151246600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:151241600-151253400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:151241600-151253400	Weak transcription	Left Ventricle	heart
49	chr1:151241800-151253200	Weak transcription	Brain Germinal Matrix	brain
50	chr1:151241800-151253400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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