Variant report

Variant	rs2890364
Chromosome Location	chr10:5833748-5833749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5831602..5838072-chr10:5842540..5850784,8	MCF-7	breast:
2	chr10:5819103..5820799-chr10:5833032..5835919,2	MCF-7	breast:
3	chr10:5832214..5833980-chr10:5854681..5856521,2	MCF-7	breast:
4	chr10:5832056..5836941-chr10:5839805..5845063,7	K562	blood:
5	chr10:5831817..5834005-chr10:5852525..5854271,2	K562	blood:

Variant related genes	Relation type
ENSG00000272764	Chromatin interaction
ENSG00000057608	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1046393	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1129614	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11596435	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11920	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17143628	0.84[EUR][1000 genomes]
rs1858446	0.97[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3793707	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs45575338	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4748572	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs55837307	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs55910451	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56033057	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56251728	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58859669	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59007376	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7095103	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72772354	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72772355	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72772358	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72772376	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72772390	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72772400	0.89[ASN][1000 genomes]
rs72774070	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72774075	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72774077	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72774078	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs74116316	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[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	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
5	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv515935	chr10:5820394-5869839	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv549896	chr10:5820394-5880066	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2890364	GDI2	cis	Artery Tibial	GTEx
rs2890364	GDI2	Cis_1M	lymphoblastoid	RTeQTL
rs2890364	GDI2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5762600-5843400	Strong transcription	Dnd41	blood
2	chr10:5762800-5843000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr10:5768000-5849400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:5797400-5847400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr10:5798000-5842800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr10:5798200-5843000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr10:5798600-5842800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr10:5805000-5843200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr10:5818000-5854200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:5818400-5842800	Strong transcription	Duodenum Mucosa	Duodenum
11	chr10:5818800-5842600	Strong transcription	Fetal Thymus	thymus
12	chr10:5819600-5844000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr10:5820200-5840400	Strong transcription	HSMM	muscle
14	chr10:5820200-5842800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr10:5820400-5843000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr10:5820400-5843000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr10:5820600-5842800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr10:5821800-5838800	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr10:5822000-5843800	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr10:5822200-5842600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr10:5822200-5843400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr10:5822400-5842600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr10:5822400-5842800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr10:5822600-5842800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr10:5822600-5842800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr10:5823600-5842600	Strong transcription	Placenta	Placenta
27	chr10:5823800-5842600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr10:5823800-5842600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr10:5823800-5843400	Strong transcription	Thymus	Thymus
30	chr10:5824000-5842600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr10:5824000-5842600	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr10:5824000-5843400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr10:5824200-5842800	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr10:5824200-5843400	Strong transcription	Fetal Intestine Large	intestine
35	chr10:5824600-5842800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr10:5824600-5843400	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr10:5825000-5842800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr10:5825400-5836200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr10:5826200-5839000	Strong transcription	HMEC	breast
40	chr10:5826400-5834000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr10:5826400-5844400	Strong transcription	Fetal Intestine Small	intestine
42	chr10:5826400-5844400	Strong transcription	Fetal Stomach	stomach
43	chr10:5826600-5843400	Strong transcription	Primary B cells from cord blood	blood
44	chr10:5826800-5842400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr10:5826800-5842800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr10:5826800-5844400	Strong transcription	Fetal Muscle Leg	muscle
47	chr10:5827200-5834200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr10:5827200-5842800	Strong transcription	GM12878-XiMat	blood
49	chr10:5827400-5842600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:5827400-5843000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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