Variant report

Variant	rs1237262
Chromosome Location	chr12:106629989-106629990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:106626541..106632087-chr12:106638755..106642966,8	MCF-7	breast:
2	chr12:106629030..106630922-chr12:106737245..106739641,2	MCF-7	breast:
3	chr12:106627619..106631130-chr12:106633186..106636182,4	MCF-7	breast:
4	chr12:106616785..106619757-chr12:106628880..106631149,2	MCF-7	breast:
5	chr12:106627724..106631160-chr12:106750781..106752959,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258355	Chromatin interaction
ENSG00000013503	Chromatin interaction
ENSG00000136026	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10459209	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs10507209	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11112908	0.89[ASN][1000 genomes]
rs11112915	0.89[ASN][1000 genomes]
rs1148413	0.91[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1148415	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1148417	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1148419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1215740	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1215741	0.95[ASN][1000 genomes]
rs1215753	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1215757	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1215759	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1215761	0.91[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1215807	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12320181	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1238021	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2649705	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2649718	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704895	0.85[ASN][1000 genomes]
rs2704896	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2704898	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2936701	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3088113	0.89[ASN][1000 genomes]
rs3782699	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830730	chr12:106621530-106642222	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv1839947	chr12:106622186-106642064	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv1797996	chr12:106622186-106642222	Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1237262	PRDM4	cis	cerebellum	SCAN
rs1237262	CCDC53	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106618000-106632000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:106618000-106632200	Weak transcription	Psoas Muscle	Psoas
3	chr12:106618600-106630600	Weak transcription	Ovary	ovary
4	chr12:106618600-106632200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:106620800-106630400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:106621200-106632000	Weak transcription	Brain Hippocampus Middle	brain
7	chr12:106621200-106632600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:106621400-106630200	Weak transcription	NHLF	lung
9	chr12:106621400-106632600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr12:106621400-106638200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:106621600-106630400	Weak transcription	HSMM	muscle
12	chr12:106621600-106630600	Weak transcription	Liver	Liver
13	chr12:106621600-106630600	Weak transcription	A549	lung
14	chr12:106621600-106631400	Weak transcription	Adipose Nuclei	Adipose
15	chr12:106621600-106631800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:106621600-106632600	Weak transcription	Colonic Mucosa	Colon
17	chr12:106621600-106632800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr12:106621800-106630400	Weak transcription	Fetal Lung	lung
19	chr12:106621800-106630600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:106621800-106630600	Weak transcription	Spleen	Spleen
21	chr12:106621800-106631800	Weak transcription	Gastric	stomach
22	chr12:106621800-106631800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:106621800-106632800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:106622000-106630000	Weak transcription	Brain Germinal Matrix	brain
25	chr12:106622000-106630600	Weak transcription	Lung	lung
26	chr12:106622000-106632200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:106622200-106632000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr12:106622200-106639000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:106622200-106639600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:106622400-106632200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr12:106622400-106632800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr12:106624400-106633000	Weak transcription	Aorta	Aorta
33	chr12:106625000-106631800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr12:106625200-106631800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr12:106625200-106631800	Weak transcription	Placenta	Placenta
36	chr12:106625200-106632600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr12:106625200-106636800	Weak transcription	Right Atrium	heart
38	chr12:106625200-106640800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr12:106625400-106630200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr12:106625400-106632600	Weak transcription	Right Ventricle	heart
41	chr12:106625400-106632600	Weak transcription	HepG2	liver
42	chr12:106625600-106630600	Weak transcription	Left Ventricle	heart
43	chr12:106625600-106632600	Weak transcription	Brain Substantia Nigra	brain
44	chr12:106626600-106631800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr12:106627000-106633000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:106627200-106631400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr12:106627400-106631000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:106627400-106631800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:106627400-106632000	Weak transcription	Fetal Intestine Large	intestine
50	chr12:106627400-106632000	Weak transcription	Rectal Mucosa Donor 29	rectum

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