Variant report

Variant	rs12488810
Chromosome Location	chr3:141703278-141703279
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10935449	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10935450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935454	0.87[EUR][1000 genomes]
rs11569177	0.87[EUR][1000 genomes]
rs11569186	0.87[EUR][1000 genomes]
rs11569193	0.89[EUR][1000 genomes]
rs11569195	0.89[EUR][1000 genomes]
rs11569202	0.87[EUR][1000 genomes]
rs11569205	0.89[EUR][1000 genomes]
rs11569206	0.89[EUR][1000 genomes]
rs11569209	0.87[EUR][1000 genomes]
rs11569214	0.89[EUR][1000 genomes]
rs11569218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11569223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11569226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569229	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11569232	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569233	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11569234	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569235	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569237	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569244	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569246	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569247	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569248	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569249	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569251	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569252	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569259	0.82[EUR][1000 genomes]
rs11569262	0.82[EUR][1000 genomes]
rs11569278	0.82[EUR][1000 genomes]
rs11705778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706402	0.89[EUR][1000 genomes]
rs11708301	0.89[EUR][1000 genomes]
rs11711960	0.89[EUR][1000 genomes]
rs11712803	0.89[EUR][1000 genomes]
rs11714727	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11716148	0.87[EUR][1000 genomes]
rs11717517	0.89[EUR][1000 genomes]
rs11718167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719793	0.89[EUR][1000 genomes]
rs11720601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493472	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12493495	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493643	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34026748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828397	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683413	0.82[EUR][1000 genomes]
rs4683414	0.82[EUR][1000 genomes]
rs4683415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683418	0.87[EUR][1000 genomes]
rs4683654	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683655	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683656	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683659	0.87[EUR][1000 genomes]
rs4683660	0.82[EUR][1000 genomes]
rs55699824	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55920121	0.84[ASN][1000 genomes]
rs56001234	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56104495	0.87[EUR][1000 genomes]
rs56162837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56184282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61397493	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637273	0.86[ASN][1000 genomes]

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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12488810	TFDP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
2	chr3:141671800-141719000	Weak transcription	Placenta	Placenta
3	chr3:141671800-141724000	Weak transcription	Right Ventricle	heart
4	chr3:141671800-141735600	Weak transcription	Aorta	Aorta
5	chr3:141674400-141708000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:141674600-141712600	Weak transcription	Fetal Brain Male	brain
7	chr3:141676200-141703800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:141677800-141739000	Weak transcription	Left Ventricle	heart
9	chr3:141678800-141745600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:141680000-141711200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:141680000-141731200	Weak transcription	Fetal Brain Female	brain
12	chr3:141680800-141723200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:141682000-141711200	Weak transcription	GM12878-XiMat	blood
14	chr3:141682600-141723400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:141682800-141712200	Weak transcription	Ovary	ovary
16	chr3:141682800-141724600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:141682800-141739000	Weak transcription	Pancreas	Pancrea
18	chr3:141682800-141745800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:141682800-141746200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr3:141683000-141719400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:141683200-141709800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:141683600-141716200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:141683800-141704600	Weak transcription	Brain Germinal Matrix	brain
24	chr3:141683800-141746600	Weak transcription	Lung	lung
25	chr3:141688000-141704800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:141688000-141719400	Strong transcription	Dnd41	blood
27	chr3:141688400-141714600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:141688800-141706200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:141688800-141711200	Weak transcription	Fetal Kidney	kidney
30	chr3:141688800-141720200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:141688800-141729000	Strong transcription	Fetal Thymus	thymus
32	chr3:141689400-141706800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:141689400-141720000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:141691400-141712200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:141691600-141706000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:141691600-141708000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:141691800-141703400	Weak transcription	Primary T cells from cord blood	blood
38	chr3:141691800-141711200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:141691800-141711400	Weak transcription	Primary B cells from cord blood	blood
40	chr3:141691800-141722800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:141692600-141712800	Weak transcription	Colon Smooth Muscle	Colon
42	chr3:141693200-141712600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr3:141694000-141704200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:141695600-141706400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:141695600-141712600	Weak transcription	Adipose Nuclei	Adipose
46	chr3:141695800-141705400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:141696400-141707600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:141696400-141719600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:141697200-141706400	Weak transcription	Fetal Stomach	stomach
50	chr3:141697200-141718800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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