Variant report

Variant	rs11124514
Chromosome Location	chr2:36621370-36621371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:36595497..36597494-chr2:36620242..36622925,2	MCF-7	breast:
2	chr2:36613783..36616310-chr2:36620739..36623500,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150938	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10178804	1.00[CHB][hapmap]
rs10186135	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10203010	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11124515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11124516	0.96[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1159133	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12465282	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12465297	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12477836	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12994926	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13394052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13407488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2689711	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3755214	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3770913	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3770924	0.92[CEU][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3770932	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3770936	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3770946	0.85[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs3770947	0.85[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4233914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4670547	1.00[CHB][hapmap]
rs4670548	0.83[EUR][1000 genomes]
rs4670554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6711707	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6755048	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs711255	1.00[JPT][hapmap]
rs7589917	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs848508	1.00[JPT][hapmap]
rs848513	1.00[JPT][hapmap]
rs848514	1.00[JPT][hapmap]
rs888075	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs888076	0.81[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9308991	1.00[CHB][hapmap]
rs9308992	1.00[CHB][hapmap]
rs997602	1.00[CHB][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	nsv833803	chr2:36589065-36745779	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11124514	THUMPD2	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36586200-36626600	Weak transcription	Primary B cells from cord blood	blood
2	chr2:36604400-36640400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:36604400-36640600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:36611600-36632400	Weak transcription	Esophagus	oesophagus
5	chr2:36611600-36635400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:36613000-36624000	Weak transcription	Small Intestine	intestine
7	chr2:36614800-36621400	Weak transcription	Stomach Mucosa	stomach
8	chr2:36616800-36624200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:36616800-36631200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:36616800-36635000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:36617000-36633400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:36617200-36622200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:36617200-36623800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:36617200-36624000	Weak transcription	Fetal Intestine Large	intestine
15	chr2:36617200-36624000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:36617200-36625000	Weak transcription	Fetal Intestine Small	intestine
17	chr2:36617200-36630800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:36617200-36631200	Weak transcription	Fetal Kidney	kidney
19	chr2:36617200-36633800	Weak transcription	Fetal Lung	lung
20	chr2:36617600-36621400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:36617600-36624000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:36617800-36630600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:36617800-36630600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:36618200-36624000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr2:36618600-36643000	Genic enhancers	Osteobl	bone
26	chr2:36619200-36621600	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr2:36619400-36621600	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr2:36619600-36621600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr2:36619600-36621800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr2:36619600-36622600	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr2:36619600-36622800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr2:36619800-36621400	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr2:36619800-36625400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:36620000-36621400	Enhancers	H1 Cell Line	embryonic stem cell
35	chr2:36620000-36621400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:36620000-36621400	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr2:36620000-36621800	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr2:36620000-36622000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:36620000-36623000	Enhancers	Hela-S3	cervix
40	chr2:36620200-36621400	Enhancers	Aorta	Aorta
41	chr2:36620200-36626400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:36620200-36635000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:36620400-36622800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:36620400-36623400	Weak transcription	Brain Germinal Matrix	brain
45	chr2:36620400-36624000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:36620800-36621600	Enhancers	Adipose Nuclei	Adipose
47	chr2:36620800-36621800	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr2:36620800-36622400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:36620800-36624000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:36620800-36629200	Genic enhancers	Muscle Satellite Cultured Cells	--

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