Variant report

Variant	rs9826925
Chromosome Location	chr3:88206392-88206393
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:88197769..88200999-chr3:88203234..88208947,7	MCF-7	breast:
2	chr3:88197032..88201570-chr3:88203720..88209497,8	K562	blood:
3	chr3:88105942..88108461-chr3:88204357..88206943,2	K562	blood:
4	chr3:88197168..88201570-chr3:88204371..88207068,4	K562	blood:

Variant related genes	Relation type
ENSG00000179021	Chromatin interaction
ENSG00000163320	Chromatin interaction
ENSG00000229729	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1006896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs10858	0.87[ASN][1000 genomes]
rs11925988	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493327	1.00[JPT][hapmap]
rs13074910	1.00[CEU][hapmap]
rs13317202	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2735559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4858934	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858939	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858940	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859003	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55883959	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs55928667	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932154	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56185750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56211058	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56246133	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6419868	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6419869	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6551276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551295	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73132512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73132546	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73146085	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs73146095	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs73146099	0.87[ASN][1000 genomes]
rs73148006	0.80[ASN][1000 genomes]
rs7430022	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7431968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7432826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432838	1.00[JPT][hapmap]
rs7610494	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7620576	0.89[EUR][1000 genomes]
rs7620830	1.00[JPT][hapmap]
rs7624215	0.91[EUR][1000 genomes]
rs7650068	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9284814	0.87[EUR][1000 genomes]
rs9865578	0.80[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9826925	LGALS14	trans	lymphoblastoid	seeQTL
rs9826925	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL
rs9826925	ZNF654	cis	lymphoblastoid	seeQTL
rs9826925	CGGBP1	cis	uninvolved skin	skin_eQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88199800-88216800	Weak transcription	Esophagus	oesophagus
2	chr3:88200800-88209400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:88200800-88214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:88200800-88218000	Weak transcription	Pancreas	Pancrea
5	chr3:88200800-88221600	Weak transcription	Psoas Muscle	Psoas
6	chr3:88200800-88224400	Weak transcription	Aorta	Aorta
7	chr3:88201200-88206400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:88201200-88209600	Weak transcription	Stomach Mucosa	stomach
9	chr3:88201400-88212200	Weak transcription	Colonic Mucosa	Colon
10	chr3:88202000-88206400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:88202000-88208200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:88202000-88208400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:88202000-88210200	Strong transcription	Placenta	Placenta
14	chr3:88202000-88211400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:88202200-88208200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:88202200-88208200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:88202200-88208200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:88202200-88208200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:88202200-88209200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:88202200-88211000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:88202200-88211800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:88202200-88212000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:88202400-88206600	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr3:88202400-88206800	Strong transcription	Fetal Lung	lung
25	chr3:88202400-88207000	Strong transcription	NH-A	brain
26	chr3:88202400-88207400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:88202400-88208000	Strong transcription	HSMM	muscle
28	chr3:88202400-88208200	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr3:88202400-88208200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:88202400-88208200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:88202400-88208200	Strong transcription	Duodenum Mucosa	Duodenum
32	chr3:88202400-88208200	Strong transcription	Fetal Intestine Large	intestine
33	chr3:88202400-88208200	Strong transcription	Osteobl	bone
34	chr3:88202400-88208400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:88202400-88208600	Strong transcription	Fetal Thymus	thymus
36	chr3:88202400-88208800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:88202400-88210000	Strong transcription	Liver	Liver
38	chr3:88202600-88206800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr3:88202600-88208400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:88202600-88209000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:88202600-88211000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:88202600-88211200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:88202800-88206800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:88202800-88208400	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:88202800-88208600	Strong transcription	Adipose Nuclei	Adipose
46	chr3:88202800-88212600	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr3:88203000-88207200	Strong transcription	Fetal Kidney	kidney
48	chr3:88203000-88207800	Strong transcription	Brain Germinal Matrix	brain
49	chr3:88203000-88208400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:88203000-88212200	Strong transcription	Primary monocytes fromperipheralblood	blood

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