Variant report

Variant	rs10939855
Chromosome Location	chr5:59930271-59930272
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:59923088..59926748-chr5:59929739..59932140,3	K562	blood:
2	chr5:59928659..59931200-chr5:59937344..59939413,2	K562	blood:
3	chr5:59928143..59930570-chr5:60056842..60058406,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000035499	Chromatin interaction
ENSG00000251303	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10939856	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11948543	0.87[ASN][1000 genomes]
rs11951503	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11952735	0.87[ASN][1000 genomes]
rs11956023	0.84[ASN][1000 genomes]
rs11959922	0.88[ASN][1000 genomes]
rs1379116	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1379117	0.88[ASN][1000 genomes]
rs153152	0.80[EUR][1000 genomes]
rs2061250	0.86[ASN][1000 genomes]
rs2198865	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs248912	0.81[EUR][1000 genomes]
rs249070	0.88[EUR][1000 genomes]
rs2591636	0.82[ASN][1000 genomes]
rs286153	0.87[ASN][1000 genomes]
rs286155	0.87[ASN][1000 genomes]
rs286156	0.81[ASN][1000 genomes]
rs286158	0.81[ASN][1000 genomes]
rs3857236	0.84[ASN][1000 genomes]
rs3958943	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4504343	0.86[EUR][1000 genomes]
rs4538566	0.86[EUR][1000 genomes]
rs4700380	0.86[ASN][1000 genomes]
rs55720622	0.84[ASN][1000 genomes]
rs55768631	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs56166952	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56191602	0.86[ASN][1000 genomes]
rs56347749	0.86[EUR][1000 genomes]
rs59155887	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62373023	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6877561	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10939855	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs10939855	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59894800-59933600	Weak transcription	Hela-S3	cervix
2	chr5:59920400-59939800	Weak transcription	HSMM	muscle
3	chr5:59920600-59947800	Weak transcription	HUVEC	blood vessel
4	chr5:59923400-59931800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:59923400-59939800	Weak transcription	K562	blood
6	chr5:59923600-59931200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:59923800-59933400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:59924400-59941800	Weak transcription	Fetal Brain Female	brain
9	chr5:59924600-59930400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:59924600-59936200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:59924800-59936400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:59925000-59942800	Strong transcription	Dnd41	blood
13	chr5:59925200-59947200	Weak transcription	Pancreas	Pancrea
14	chr5:59926000-59933800	Strong transcription	Fetal Intestine Large	intestine
15	chr5:59926200-59933400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:59926400-59967800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:59926600-59946200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:59926800-59930800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:59927200-59944000	Weak transcription	Fetal Muscle Leg	muscle
20	chr5:59927400-59930600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:59927400-59931400	Weak transcription	Primary B cells from cord blood	blood
22	chr5:59927400-59933000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr5:59927400-59935200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:59927400-59941200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:59927600-59933000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr5:59928200-59930800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr5:59928400-59942800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr5:59928600-59935800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:59929200-59933000	Weak transcription	Fetal Stomach	stomach
30	chr5:59929400-59931000	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr5:59929400-59932600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr5:59929400-59933000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:59929400-59934600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:59929400-59942800	Weak transcription	Fetal Intestine Small	intestine
35	chr5:59929400-59944400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr5:59929400-59947400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr5:59929400-59954600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:59929600-59930400	Weak transcription	A549	lung
39	chr5:59929600-59933000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:59929600-59933400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr5:59929600-59933600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:59929600-59935200	Weak transcription	Fetal Thymus	thymus
43	chr5:59929600-59948000	Weak transcription	NHEK	skin
44	chr5:59929800-59932400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr5:59929800-59933200	Weak transcription	HMEC	breast
46	chr5:59930000-59930800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:59930000-59931800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:59930000-59931800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr5:59930000-59933600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr5:59930000-59933800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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