Variant report

Variant	rs9942410
Chromosome Location	chr5:59995820-59995821
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:59994096..59995835-chr5:60107793..60109955,2	MCF-7	breast:
2	chr5:59994474..59997876-chr5:60455928..60460228,5	K562	blood:
3	chr5:59995106..59997535-chr5:60240120..60242292,3	K562	blood:
4	chr5:59993591..59996148-chr5:60625919..60628980,4	K562	blood:
5	chr5:59994210..59996553-chr5:60627404..60629725,2	MCF-7	breast:
6	chr5:59994332..59996148-chr5:60627447..60629730,3	K562	blood:

Variant related genes	Relation type
ENSG00000188725	Chromatin interaction
ENSG00000130449	Chromatin interaction
ENSG00000164182	Chromatin interaction
ENSG00000251279	Chromatin interaction
ENSG00000049167	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10043291	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs10050803	0.89[CEU][hapmap]
rs10058456	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs10805370	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs10939858	0.90[ASN][1000 genomes]
rs10939860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10939862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11739724	0.82[EUR][1000 genomes]
rs11740327	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs11741754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11745627	0.83[EUR][1000 genomes]
rs11948543	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes]
rs11952735	0.84[EUR][1000 genomes]
rs11955398	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11956023	0.89[EUR][1000 genomes]
rs11959922	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs12186391	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12514253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12515025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12517174	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12517207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12522801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12655515	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1379114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1379115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1379116	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1379117	0.86[EUR][1000 genomes]
rs1444237	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs1456742	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1456743	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1460958	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs1562235	0.84[EUR][1000 genomes]
rs17387940	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1816899	0.83[EUR][1000 genomes]
rs1824120	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1870014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1992612	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2045356	0.86[CEU][hapmap]
rs2061250	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes]
rs206789	0.82[CHB][hapmap]
rs2085409	0.81[ASN][1000 genomes]
rs2085410	0.81[EUR][1000 genomes]
rs2085411	0.81[EUR][1000 genomes]
rs2085413	0.81[EUR][1000 genomes]
rs2100584	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2409792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2409794	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs286153	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs286154	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs286158	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs2898287	0.83[EUR][1000 genomes]
rs2898288	0.81[ASN][1000 genomes]
rs3857236	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs4277863	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4447941	0.81[EUR][1000 genomes]
rs4524466	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4538567	0.80[EUR][1000 genomes]
rs4700380	0.85[EUR][1000 genomes]
rs55720622	0.84[EUR][1000 genomes]
rs55854817	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56191602	0.87[EUR][1000 genomes]
rs56726435	0.93[ASN][1000 genomes]
rs57521726	0.82[EUR][1000 genomes]
rs62373024	0.84[EUR][1000 genomes]
rs62373025	0.83[EUR][1000 genomes]
rs6449483	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs6449485	0.82[EUR][1000 genomes]
rs6449487	0.85[EUR][1000 genomes]
rs6449493	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6874072	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs755077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7701708	0.81[EUR][1000 genomes]
rs7707698	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7720233	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs7730342	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7736518	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs897672	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs930864	0.80[ASN][1000 genomes]
rs9686489	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv508362	chr5:59990308-60050894	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	esv1816307	chr5:59992305-60012235	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	esv1794154	chr5:59995393-60012235	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	esv1821070	chr5:59995393-60012235	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	esv1801919	chr5:59995393-60013913	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9942410	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59992600-59996600	Active TSS	GM12878-XiMat	blood
2	chr5:59993000-59996400	Active TSS	Placenta	Placenta
3	chr5:59994200-59996400	Active TSS	Fetal Kidney	kidney
4	chr5:59994200-59996600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:59994200-59996800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:59994400-59996200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:59994400-59996600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:59994400-59996600	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr5:59994400-59996600	Active TSS	K562	blood
10	chr5:59994400-59996800	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr5:59994400-59996800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:59994400-59997000	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr5:59994600-59996600	Active TSS	H1 Cell Line	embryonic stem cell
14	chr5:59994600-59996800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:59994600-59996800	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr5:59994600-59996800	Active TSS	NHLF	lung
17	chr5:59994800-59996600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr5:59994800-59996600	Active TSS	H9 Cell Line	embryonic stem cell
19	chr5:59994800-59996600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:59994800-59996600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:59994800-59996600	Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr5:59994800-59996600	Active TSS	Fetal Intestine Small	intestine
23	chr5:59994800-59996800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:59994800-59996800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:59994800-59996800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:59994800-59996800	Active TSS	HSMM	muscle
27	chr5:59994800-59996800	Active TSS	HSMMtube	muscle
28	chr5:59994800-59996800	Active TSS	NHDF-Ad	bronchial
29	chr5:59994800-59997000	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr5:59994800-59997000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:59994800-59997000	Active TSS	Fetal Brain Female	brain
32	chr5:59994800-59997000	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr5:59995000-59996200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr5:59995000-59996200	Active TSS	Hela-S3	cervix
35	chr5:59995000-59996200	Active TSS	HMEC	breast
36	chr5:59995000-59996400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:59995000-59996400	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr5:59995000-59996400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:59995000-59996400	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr5:59995000-59996400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:59995000-59996400	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr5:59995000-59996400	Bivalent/Poised TSS	HepG2	liver
43	chr5:59995000-59996600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr5:59995000-59996600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:59995000-59996600	Active TSS	Muscle Satellite Cultured Cells	--
46	chr5:59995000-59996600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:59995000-59996600	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr5:59995000-59996600	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr5:59995000-59996600	Active TSS	Fetal Intestine Large	intestine
50	chr5:59995000-59996600	Active TSS	Stomach Mucosa	stomach

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