Variant report

Variant	rs12145131
Chromosome Location	chr1:212960137-212960138
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212781016..212783376-chr1:212959692..212961449,2	MCF-7	breast:
2	chr1:212955485..212957431-chr1:212958159..212961189,3	K562	blood:
3	chr1:212958789..212962181-chr1:212964353..212966610,4	K562	blood:

Variant related genes	Relation type
ENSG00000117697	Chromatin interaction
ENSG00000203705	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10127512	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10127703	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10127756	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1046083	0.92[AFR][1000 genomes]
rs10863988	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10863997	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11120006	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11120010	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11120014	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11120017	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11120018	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11556187	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11806535	0.81[ASN][1000 genomes]
rs11808846	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11809232	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11809382	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11811017	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12125867	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12128903	0.81[AMR][1000 genomes]
rs12129465	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12133174	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12137768	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12402370	0.86[ASN][1000 genomes]
rs12404618	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12404885	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12406499	0.81[ASN][1000 genomes]
rs12409787	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13376317	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13376383	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13376390	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1507357	0.81[ASN][1000 genomes]
rs1507358	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1857971	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2135823	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2174781	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28872849	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34110137	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3738798	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738803	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs55840547	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56088044	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56243109	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57449384	0.86[ASN][1000 genomes]
rs58203936	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59231663	0.81[AMR][1000 genomes]
rs60308869	0.94[AFR][1000 genomes]
rs61736926	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540760	0.90[AFR][1000 genomes]
rs6540762	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6657089	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6664049	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6665365	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6670648	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6671866	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6687672	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6688238	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6694448	0.90[AFR][1000 genomes]
rs6700204	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6702101	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73081830	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73081853	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73081902	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73083705	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73083707	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73083727	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73083731	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73083743	0.88[ASN][1000 genomes]
rs73083749	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7516312	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7527216	0.94[AFR][1000 genomes]
rs7536456	0.96[EUR][1000 genomes]
rs7537598	0.87[ASN][1000 genomes]
rs7538755	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7546754	0.92[AFR][1000 genomes]
rs7550288	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7552880	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7552899	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv1010003	chr1:212944240-212986996	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12145131	TATDN3	cis	Adipose Subcutaneous	GTEx
rs12145131	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212895400-212964600	Weak transcription	Pancreas	Pancrea
2	chr1:212895600-212964600	Weak transcription	Gastric	stomach
3	chr1:212923600-212963800	Weak transcription	Brain Angular Gyrus	brain
4	chr1:212923600-212964400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:212923800-212964200	Weak transcription	HMEC	breast
6	chr1:212926600-212963400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:212927400-212963400	Weak transcription	Small Intestine	intestine
8	chr1:212927400-212964200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:212936600-212960200	Weak transcription	Lung	lung
10	chr1:212936600-212964400	Weak transcription	Esophagus	oesophagus
11	chr1:212941200-212964200	Weak transcription	Right Ventricle	heart
12	chr1:212942400-212964200	Weak transcription	Aorta	Aorta
13	chr1:212942600-212964400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:212942800-212964200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:212943200-212964200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:212944200-212964400	Weak transcription	Fetal Heart	heart
17	chr1:212950400-212964200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:212951800-212964400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:212952400-212963000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:212952600-212963600	Weak transcription	Colonic Mucosa	Colon
21	chr1:212953000-212964400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:212953200-212964400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:212953800-212960200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:212953800-212960200	Strong transcription	HSMM	muscle
25	chr1:212953800-212961000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:212954000-212960600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:212954000-212960600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:212954000-212960600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:212954000-212960800	Strong transcription	Placenta	Placenta
30	chr1:212954000-212961000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:212954000-212961000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:212954000-212961000	Strong transcription	Liver	Liver
33	chr1:212954000-212961000	Strong transcription	Fetal Thymus	thymus
34	chr1:212954000-212961200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:212954000-212961200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:212954200-212960400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr1:212954200-212960600	Strong transcription	Primary B cells from cord blood	blood
38	chr1:212954200-212960600	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:212954200-212960600	Strong transcription	K562	blood
40	chr1:212954200-212960800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr1:212954200-212960800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:212954200-212961000	Strong transcription	Dnd41	blood
43	chr1:212954200-212961600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:212954400-212964400	Weak transcription	Spleen	Spleen
45	chr1:212954600-212960400	Strong transcription	Fetal Intestine Large	intestine
46	chr1:212954600-212960600	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr1:212954800-212960800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:212954800-212961000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:212955000-212961000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:212955000-212961400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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