Variant report

Variant	rs12231670
Chromosome Location	chr12:30812798-30812799
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:30812418..30814801-chr7:127470835..127472989,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10431223	0.84[EUR][1000 genomes]
rs11050960	0.84[EUR][1000 genomes]
rs11050962	0.84[EUR][1000 genomes]
rs11050963	0.84[EUR][1000 genomes]
rs11050964	0.84[EUR][1000 genomes]
rs11050965	0.84[EUR][1000 genomes]
rs11050975	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11050976	0.84[EUR][1000 genomes]
rs11050978	0.84[EUR][1000 genomes]
rs11050979	0.84[EUR][1000 genomes]
rs11050980	0.84[EUR][1000 genomes]
rs11050981	0.84[EUR][1000 genomes]
rs11050982	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11050995	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11050996	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050997	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050998	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050999	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11051000	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11051001	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11051004	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11051011	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051014	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051016	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051017	1.00[ASN][1000 genomes]
rs11051021	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11051024	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051025	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051031	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051032	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051036	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11051039	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11051040	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11051043	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11051057	1.00[AMR][1000 genomes]
rs11051060	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11051064	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11051067	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11051074	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11534760	0.84[EUR][1000 genomes]
rs11561156	0.84[EUR][1000 genomes]
rs1157125	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12228212	0.84[EUR][1000 genomes]
rs12229358	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12229986	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12230006	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12230490	0.84[EUR][1000 genomes]
rs16906574	0.84[EUR][1000 genomes]
rs16906582	0.84[EUR][1000 genomes]
rs16906596	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16906601	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16906606	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16906713	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16906758	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16916147	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2101288	1.00[AMR][1000 genomes]
rs2114900	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3850958	0.84[EUR][1000 genomes]
rs3850959	0.84[ASN][1000 genomes]
rs3889761	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57735299	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60712960	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7970293	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7977562	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv515645	chr12:30810826-30812828	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30767000-30844200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:30775600-30815400	Weak transcription	Right Ventricle	heart
3	chr12:30775800-30813200	Weak transcription	HMEC	breast
4	chr12:30775800-30815200	Weak transcription	NHEK	skin
5	chr12:30779800-30825000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:30780800-30847000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:30781800-30826400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:30782400-30814800	Weak transcription	Brain Angular Gyrus	brain
9	chr12:30782400-30821200	Weak transcription	Esophagus	oesophagus
10	chr12:30783800-30827400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:30783800-30829000	Weak transcription	Small Intestine	intestine
12	chr12:30784000-30815800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:30784800-30836600	Weak transcription	Fetal Heart	heart
14	chr12:30785000-30847800	Weak transcription	Gastric	stomach
15	chr12:30785200-30846400	Weak transcription	Spleen	Spleen
16	chr12:30785400-30847200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:30785800-30813200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:30786000-30813000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:30786000-30826600	Weak transcription	Colonic Mucosa	Colon
20	chr12:30787200-30813000	Weak transcription	Ovary	ovary
21	chr12:30787200-30813400	Weak transcription	Brain Substantia Nigra	brain
22	chr12:30787200-30821200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:30788000-30821000	Weak transcription	Stomach Mucosa	stomach
24	chr12:30790000-30813000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr12:30790200-30813000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:30790400-30813200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:30791200-30815600	Weak transcription	Fetal Brain Female	brain
28	chr12:30791200-30825200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:30792000-30813200	Weak transcription	Psoas Muscle	Psoas
30	chr12:30793600-30825200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr12:30794200-30813200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:30796800-30812800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr12:30796800-30816000	Weak transcription	NHLF	lung
34	chr12:30797000-30815200	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:30797200-30813000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:30798400-30813200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:30798600-30814800	Weak transcription	HepG2	liver
38	chr12:30799200-30813200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr12:30801400-30815600	Weak transcription	Brain Germinal Matrix	brain
40	chr12:30802400-30813200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:30802400-30813200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:30802400-30813200	Weak transcription	Osteobl	bone
43	chr12:30802600-30813200	Weak transcription	HSMM	muscle
44	chr12:30803800-30813200	Weak transcription	K562	blood
45	chr12:30804600-30815000	Weak transcription	Fetal Brain Male	brain
46	chr12:30805200-30813200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:30805200-30813200	Weak transcription	Fetal Kidney	kidney
48	chr12:30805400-30813200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr12:30805600-30813200	Weak transcription	GM12878-XiMat	blood
50	chr12:30805800-30813200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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