Variant report

Variant	rs2404295
Chromosome Location	chr9:97723868-97723869
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97688111..97690470-chr9:97723342..97725072,2	MCF-7	breast:
2	chr9:97716548..97719143-chr9:97721802..97724733,2	K562	blood:
3	chr9:97722921..97724828-chr9:97727908..97729836,2	K562	blood:
4	chr9:97723418..97725512-chr9:97771283..97773130,2	MCF-7	breast:
5	chr9:97688635..97691116-chr9:97722109..97725030,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1004373	0.87[JPT][hapmap]
rs10119512	0.87[CHD][hapmap];0.87[JPT][hapmap]
rs10512253	0.87[JPT][hapmap]
rs10761364	0.81[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10761366	0.81[AMR][1000 genomes]
rs10993427	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10993435	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs10993449	0.88[YRI][hapmap]
rs1113102	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1564234	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1571894	0.87[JPT][hapmap];0.81[AMR][1000 genomes]
rs1571895	0.84[CHD][hapmap];0.87[JPT][hapmap]
rs2061800	0.87[JPT][hapmap];0.81[AMR][1000 genomes]
rs2404302	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs2404305	0.87[CHD][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes]
rs2404456	0.87[JPT][hapmap]
rs3802454	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3802456	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4537362	0.87[JPT][hapmap];0.81[AMR][1000 genomes]
rs4743979	0.87[JPT][hapmap]
rs4743984	0.81[CEU][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap]
rs4744423	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4744424	0.87[JPT][hapmap]
rs4744425	0.86[JPT][hapmap]
rs4744426	0.87[CHD][hapmap];0.87[JPT][hapmap]
rs4744430	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs4744432	0.87[JPT][hapmap]
rs4744433	0.87[JPT][hapmap]
rs6479591	0.87[CHD][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes]
rs6479592	0.87[JPT][hapmap];0.81[AMR][1000 genomes]
rs7020709	0.87[JPT][hapmap]
rs7021351	0.87[CHD][hapmap];0.87[JPT][hapmap]
rs7022452	0.87[CHD][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes]
rs7042271	0.84[ASW][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs7048786	0.87[CHD][hapmap];0.87[JPT][hapmap]
rs7048941	0.87[CHD][hapmap];0.87[JPT][hapmap]
rs7851173	0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs7862156	0.81[CEU][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap]
rs7863291	0.87[CHD][hapmap];0.87[JPT][hapmap]
rs7865144	0.80[ASN][1000 genomes]
rs962229	0.87[JPT][hapmap]

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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1045849	chr9:97688810-97741336	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2404295	FOXE1	cis	parietal	SCAN
rs2404295	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:97709200-97730400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:97713400-97726200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:97713800-97757400	Weak transcription	Fetal Brain Female	brain
5	chr9:97714200-97734200	Weak transcription	Lung	lung
6	chr9:97714200-97735800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:97715000-97735600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr9:97715000-97758200	Weak transcription	Spleen	Spleen
9	chr9:97715200-97732200	Weak transcription	Ovary	ovary
10	chr9:97715200-97734600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:97715200-97748200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr9:97715400-97735800	Weak transcription	Right Ventricle	heart
13	chr9:97715400-97741200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr9:97715400-97749600	Weak transcription	Thymus	Thymus
15	chr9:97715600-97724200	Weak transcription	NHLF	lung
16	chr9:97715600-97730000	Weak transcription	Hela-S3	cervix
17	chr9:97715600-97742000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr9:97715600-97742000	Weak transcription	Psoas Muscle	Psoas
19	chr9:97715600-97742400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr9:97715800-97724000	Weak transcription	Brain Substantia Nigra	brain
21	chr9:97715800-97735600	Weak transcription	NHDF-Ad	bronchial
22	chr9:97716000-97724000	Weak transcription	Brain Angular Gyrus	brain
23	chr9:97716000-97724000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr9:97716000-97729400	Weak transcription	Fetal Kidney	kidney
25	chr9:97716000-97735200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr9:97716000-97742400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr9:97716200-97724200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr9:97716200-97734000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:97716200-97734000	Weak transcription	Left Ventricle	heart
30	chr9:97716200-97735200	Weak transcription	NH-A	brain
31	chr9:97716200-97735400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr9:97716600-97734200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr9:97716600-97735800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:97716800-97732400	Weak transcription	Fetal Heart	heart
35	chr9:97718200-97724000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:97718400-97724000	Weak transcription	Fetal Lung	lung
37	chr9:97718800-97736800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr9:97718800-97744000	Weak transcription	GM12878-XiMat	blood
39	chr9:97719000-97724000	Weak transcription	Brain Anterior Caudate	brain
40	chr9:97719000-97730000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr9:97719000-97733400	Weak transcription	Primary B cells from cord blood	blood
42	chr9:97719000-97733800	Weak transcription	Aorta	Aorta
43	chr9:97719000-97734000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr9:97719000-97735600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr9:97719000-97735800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr9:97719000-97743400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr9:97719000-97745800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr9:97719200-97725200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr9:97719200-97729600	Weak transcription	Fetal Intestine Small	intestine
50	chr9:97719200-97732600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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