Variant report

Variant	rs11955398
Chromosome Location	chr5:59981085-59981086
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:59976157..59978303-chr5:59980094..59983522,3	K562	blood:
2	chr5:59974424..59976131-chr5:59981029..59983580,2	MCF-7	breast:
3	chr5:59979528..59981743-chr5:60138984..60140817,2	K562	blood:
4	chr5:59978724..59981449-chr5:59990551..59993454,2	K562	blood:
5	chr5:59975344..59978303-chr5:59980316..59982465,2	K562	blood:

Variant related genes	Relation type
ENSG00000164181	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10043291	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10058456	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs10062240	0.88[CEU][hapmap]
rs10939858	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10939860	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[ASN][1000 genomes]
rs10939862	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11740327	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs11741754	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948543	0.91[CHB][hapmap];0.98[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap]
rs11954496	0.81[ASN][1000 genomes]
rs11959922	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs12186391	0.97[ASN][1000 genomes]
rs12514253	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12515025	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[ASN][1000 genomes]
rs12517174	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12517207	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12522801	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1379114	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.99[ASN][1000 genomes]
rs1379115	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1379116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1444237	0.88[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs1456742	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1456743	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1460958	0.87[ASW][hapmap];0.85[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap]
rs17387940	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1807017	0.84[CEU][hapmap]
rs1824120	0.99[ASN][1000 genomes]
rs1870014	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[ASN][1000 genomes]
rs1992612	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs2061250	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs206789	0.82[CHD][hapmap]
rs2085409	0.85[ASN][1000 genomes]
rs2085410	0.81[ASN][1000 genomes]
rs2085411	0.83[ASN][1000 genomes]
rs2085413	0.83[ASN][1000 genomes]
rs2100584	0.85[ASN][1000 genomes]
rs2198865	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2409792	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.99[ASN][1000 genomes]
rs2409794	0.85[ASN][1000 genomes]
rs286153	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs286154	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs286158	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs2898288	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3857236	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs4133470	0.90[YRI][hapmap]
rs4277863	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4447941	0.82[ASN][1000 genomes]
rs4524466	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs55854817	0.96[ASN][1000 genomes]
rs56191602	0.80[ASN][1000 genomes]
rs56726435	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59155887	0.82[EUR][1000 genomes]
rs6449490	0.81[ASN][1000 genomes]
rs6449491	0.81[ASN][1000 genomes]
rs6449493	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs6874699	0.88[CEU][hapmap]
rs6882727	0.81[ASN][1000 genomes]
rs755077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7701708	0.83[ASN][1000 genomes]
rs7704338	0.85[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs7707698	0.97[ASN][1000 genomes]
rs7709056	0.81[EUR][1000 genomes]
rs7719611	0.85[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs7720233	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7730342	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7736518	0.92[ASN][1000 genomes]
rs930864	0.84[ASN][1000 genomes]
rs9686489	0.97[ASN][1000 genomes]
rs9942410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv462198	chr5:59969015-60116613	Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv598298	chr5:59969015-60116613	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1023403	chr5:59969534-60079822	Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv4850	chr5:59976186-60039810	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv968833	chr5:59976941-59986267	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11955398	DEPDC1B	cis	cerebellum	SCAN
rs11955398	ELOVL7	cis	parietal	SCAN
rs11955398	ERCC8	Cis_1M	lymphoblastoid	RTeQTL
rs11955398	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59956800-59981800	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr5:59962600-59981600	Weak transcription	Fetal Muscle Leg	muscle
3	chr5:59962600-59985600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr5:59962600-59986800	Weak transcription	Fetal Stomach	stomach
5	chr5:59962600-59990000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr5:59966000-59988800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:59967400-59981800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:59968000-59981800	Weak transcription	Thymus	Thymus
9	chr5:59969400-59981400	Weak transcription	GM12878-XiMat	blood
10	chr5:59969600-59984000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:59969600-59994800	Weak transcription	Fetal Lung	lung
12	chr5:59970600-59981600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:59971000-59993800	Weak transcription	NHLF	lung
14	chr5:59971000-59994000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr5:59971000-59994200	Weak transcription	NH-A	brain
16	chr5:59971200-59981800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:59972400-59983200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:59973000-59984200	Weak transcription	Small Intestine	intestine
19	chr5:59973200-59985400	Weak transcription	HMEC	breast
20	chr5:59973600-59986000	Weak transcription	Primary B cells from cord blood	blood
21	chr5:59973800-59986600	Weak transcription	Osteobl	bone
22	chr5:59974000-59981600	Weak transcription	NHEK	skin
23	chr5:59974200-59984200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:59974200-59994200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr5:59974400-59993600	Weak transcription	Hela-S3	cervix
26	chr5:59975400-59983800	Weak transcription	A549	lung
27	chr5:59977200-59981800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:59977200-59991000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr5:59977200-59991200	Weak transcription	Pancreas	Pancrea
30	chr5:59977200-59994800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr5:59977400-59984600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr5:59977600-59981800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr5:59977600-59983200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:59978600-59983200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr5:59978800-59983200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:59978800-59984200	Strong transcription	Dnd41	blood
37	chr5:59979000-59981800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:59979200-59985000	Weak transcription	Fetal Brain Female	brain
39	chr5:59979600-59981600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr5:59980000-59981800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:59980000-59983200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr5:59980000-59983800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:59980200-59982800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:59980200-59982800	Strong transcription	HepG2	liver
45	chr5:59980200-59995200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr5:59980400-59982800	Strong transcription	Primary hematopoietic stem cells	blood
47	chr5:59980600-59981600	Strong transcription	K562	blood
48	chr5:59980800-59981200	Enhancers	Fetal Kidney	kidney
49	chr5:59980800-59983000	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr5:59980800-59983000	Strong transcription	HUES6 Cell Line	embryonic stem cell

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