Variant report

Variant	rs2414501
Chromosome Location	chr15:57613121-57613122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:57596677..57601983-chr15:57611239..57618411,9	K562	blood:
2	chr15:57022824..57027100-chr15:57611258..57614634,3	K562	blood:
3	chr15:57592002..57594571-chr15:57612516..57615928,4	K562	blood:
4	chr15:57610844..57612856-chr15:57612872..57614940,2	K562	blood:
5	chr15:57209252..57213677-chr15:57612967..57616292,5	K562	blood:
6	chr15:57022824..57025649-chr15:57612283..57614634,3	K562	blood:
7	chr15:57574448..57575948-chr15:57613094..57616013,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCF12-2	chr15:57612991-57613157	ENSG00000260172.1

No data

Variant related genes	Relation type
ENSG00000137871	Chromatin interaction
ENSG00000260172	Chromatin interaction
ENSG00000140262	Chromatin interaction
ENSG00000247982	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10459625	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11071311	0.90[ASW][hapmap];0.88[CEU][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11631073	0.91[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855537	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12904145	0.91[CEU][hapmap];0.86[AFR][1000 genomes]
rs12905158	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs12913286	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12917506	0.86[CHB][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs17820184	0.92[CEU][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs2431018	0.88[CEU][hapmap]
rs2544132	0.92[CEU][hapmap]
rs2591053	0.87[EUR][1000 genomes]
rs2591054	0.87[CEU][hapmap]
rs4534776	0.81[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs4774256	0.81[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4774924	0.88[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4774926	0.81[ASW][hapmap];0.81[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4774927	0.88[CEU][hapmap];0.85[JPT][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4774928	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61999614	0.88[EUR][1000 genomes]
rs61999616	0.82[ASN][1000 genomes]
rs61999617	0.82[ASN][1000 genomes]
rs749248	0.81[ASN][1000 genomes]
rs8027325	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv3359786	chr15:57611310-57613808	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2414501	TEX9	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57599600-57614200	Weak transcription	Small Intestine	intestine
2	chr15:57599600-57617800	Weak transcription	Spleen	Spleen
3	chr15:57602800-57617000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:57605000-57619400	Weak transcription	Pancreas	Pancrea
5	chr15:57605600-57614400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr15:57611200-57615000	Enhancers	Fetal Muscle Trunk	muscle
7	chr15:57611400-57616400	Enhancers	Fetal Muscle Leg	muscle
8	chr15:57611400-57620600	Enhancers	Fetal Intestine Small	intestine
9	chr15:57611800-57613200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:57611800-57613200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr15:57612000-57614000	Enhancers	K562	blood
12	chr15:57612000-57615800	Enhancers	Fetal Intestine Large	intestine
13	chr15:57612200-57613200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr15:57612400-57613200	Enhancers	Ovary	ovary
15	chr15:57612400-57613200	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr15:57612400-57613400	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr15:57612400-57613600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:57612400-57613600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr15:57612400-57617800	Enhancers	Fetal Thymus	thymus
20	chr15:57612600-57613200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:57612600-57613200	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr15:57612600-57613200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr15:57612600-57613200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:57612600-57613400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:57612600-57613400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:57612600-57613600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:57612600-57613600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr15:57612600-57613600	Enhancers	Brain Anterior Caudate	brain
29	chr15:57612600-57613600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr15:57612600-57613600	Enhancers	NHDF-Ad	bronchial
31	chr15:57612600-57613600	Enhancers	Osteobl	bone
32	chr15:57612600-57613800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:57612600-57615200	Weak transcription	Colonic Mucosa	Colon
34	chr15:57612600-57616000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:57612600-57616400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr15:57612600-57616400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:57612600-57616400	Weak transcription	Fetal Brain Male	brain
38	chr15:57612600-57616400	Enhancers	HUVEC	blood vessel
39	chr15:57612600-57617600	Enhancers	Stomach Mucosa	stomach
40	chr15:57612800-57613200	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr15:57612800-57613200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:57612800-57613200	Enhancers	Primary B cells from cord blood	blood
43	chr15:57612800-57613200	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr15:57612800-57613200	Enhancers	A549	lung
45	chr15:57612800-57613200	Enhancers	HSMM	muscle
46	chr15:57612800-57613200	Flanking Active TSS	NH-A	brain
47	chr15:57612800-57613400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr15:57612800-57613400	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr15:57612800-57613400	Enhancers	Brain Cingulate Gyrus	brain
50	chr15:57612800-57613400	Enhancers	GM12878-XiMat	blood

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