Variant report

Variant	rs17512142
Chromosome Location	chr12:118623991-118623992
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:118623962..118626821-chr12:118810133..118812850,4	MCF-7	breast:
2	chr12:118618995..118624149-chr12:118809534..118814465,7	K562	blood:
3	chr12:118616609..118618559-chr12:118621695..118624437,2	K562	blood:

Variant related genes	Relation type
ENSG00000135090	Chromatin interaction
ENSG00000111707	Chromatin interaction
ENSG00000270482	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10507286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850967	0.85[CEU][hapmap]
rs11068891	0.92[CEU][hapmap]
rs11068908	0.92[CEU][hapmap]
rs11068917	0.92[CEU][hapmap]
rs11068919	0.85[CEU][hapmap]
rs12229607	0.92[CEU][hapmap]
rs12820035	1.00[CHB][hapmap]
rs16939761	1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs16948179	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs16948193	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16948197	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16948204	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs16948230	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16948234	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs16948250	0.85[CEU][hapmap]
rs17433217	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17440315	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs17440336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs17440364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17440433	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17440669	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs17440774	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17440823	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17440893	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap]
rs17512177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17512198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17512219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17512407	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17512483	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17512525	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17512574	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs17512609	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap]
rs17512644	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap]
rs17512652	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs17586342	1.00[CEU][hapmap]
rs17619932	0.92[CEU][hapmap]
rs2062519	0.85[CEU][hapmap]
rs2280711	1.00[CEU][hapmap]
rs2784	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3852531	1.00[ASN][1000 genomes]
rs3852532	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766899	0.85[CEU][hapmap]
rs4766900	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap]
rs55833534	0.81[EUR][1000 genomes]
rs56033674	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56708462	0.81[EUR][1000 genomes]
rs5745799	1.00[ASW][hapmap]
rs5745876	1.00[ASW][hapmap]
rs58113338	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943362	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61943525	0.81[AMR][1000 genomes]
rs61943535	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943537	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61943538	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945177	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945180	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945181	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945182	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945183	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945184	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945187	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945188	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945189	1.00[ASN][1000 genomes]
rs61945190	1.00[ASN][1000 genomes]
rs61945192	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945206	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945210	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945212	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945216	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945217	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945220	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945221	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945223	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61945224	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61945225	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61946064	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61946067	0.82[AMR][1000 genomes]
rs61946068	0.82[AMR][1000 genomes]
rs6490173	0.92[CEU][hapmap]
rs6490177	0.82[CEU][hapmap]
rs673078	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7136216	1.00[CEU][hapmap]
rs7294498	0.85[CEU][hapmap]
rs7299040	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap]
rs7301950	1.00[ASN][1000 genomes]
rs7302387	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7303417	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307393	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs7309671	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs7314987	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73205512	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73205526	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73205531	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7954330	1.00[ASN][1000 genomes]
rs7961312	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7962185	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7963353	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965350	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967900	1.00[ASW][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap]
rs7970481	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977403	1.00[ASN][1000 genomes]
rs7980093	1.00[JPT][hapmap]
rs884844	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap]
rs9943819	0.92[CEU][hapmap]

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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1054703	chr12:118575000-118638613	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv541611	chr12:118575000-118638613	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1035497	chr12:118599539-118732144	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv541612	chr12:118599539-118732144	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17512142	POP5	cis	parietal	SCAN
rs17512142	SUDS3	cis	cerebellum	SCAN
rs17512142	SUDS3	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118576000-118624000	Weak transcription	Stomach Mucosa	stomach
2	chr12:118584000-118627600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:118599800-118625600	Weak transcription	Pancreas	Pancrea
4	chr12:118603600-118625400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:118610200-118624000	Weak transcription	Small Intestine	intestine
6	chr12:118610600-118625400	Weak transcription	Psoas Muscle	Psoas
7	chr12:118610600-118627600	Weak transcription	Esophagus	oesophagus
8	chr12:118612400-118626800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:118614400-118625600	Weak transcription	Right Ventricle	heart
10	chr12:118615200-118625400	Weak transcription	K562	blood
11	chr12:118617200-118625600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:118617200-118625600	Weak transcription	NH-A	brain
13	chr12:118617200-118634400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:118617400-118625400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:118619200-118625000	Weak transcription	Aorta	Aorta
16	chr12:118619200-118625600	Weak transcription	Placenta	Placenta
17	chr12:118619200-118626600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:118619200-118627600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:118619200-118638600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:118619400-118624000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:118619400-118624600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:118619400-118625400	Weak transcription	HSMMtube	muscle
23	chr12:118619400-118625600	Weak transcription	Ovary	ovary
24	chr12:118619400-118626200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:118619400-118626600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr12:118619400-118626600	Weak transcription	Left Ventricle	heart
27	chr12:118619400-118626800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:118619400-118626800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:118619400-118627400	Weak transcription	Lung	lung
30	chr12:118619400-118627600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:118619400-118627600	Weak transcription	Colonic Mucosa	Colon
32	chr12:118619400-118635200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:118619400-118635800	Weak transcription	Gastric	stomach
34	chr12:118619400-118635800	Weak transcription	Spleen	Spleen
35	chr12:118619600-118624400	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr12:118619600-118624800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr12:118619600-118625400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:118619600-118625400	Weak transcription	Primary T cells from cord blood	blood
39	chr12:118619600-118625400	Weak transcription	Fetal Muscle Leg	muscle
40	chr12:118619600-118625400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:118619600-118625600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:118619600-118625600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr12:118619600-118625600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:118619600-118625600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr12:118619600-118625600	Weak transcription	Thymus	Thymus
46	chr12:118619600-118631000	Weak transcription	Fetal Thymus	thymus
47	chr12:118619600-118632800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr12:118619600-118635800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:118619800-118625400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr12:118619800-118625800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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