Variant report

Variant	rs1621388
Chromosome Location	chr12:121622563-121622564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:121622296-121622620	NHEK	skin:	n/a	n/a
2	CTCF	chr12:121622440-121622590	NHEK	skin:	n/a	n/a
3	MYC	chr12:121622233-121622564	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:121622459..121624219-chr12:121638414..121640723,2	MCF-7	breast:
2	chr12:121612772..121615002-chr12:121621675..121623747,2	K562	blood:
3	chr12:121604306..121607108-chr12:121620261..121622933,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261827	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11065468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065469	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065470	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065471	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1618709	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1619628	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626329	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653601	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653602	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653603	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653605	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1653610	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653611	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1653612	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653614	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653616	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653617	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653618	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718130	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1718131	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718132	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718133	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1718134	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1718135	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718136	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718137	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1718160	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2567986	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2567988	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2567989	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2567991	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2567997	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2567999	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2568001	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568003	0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2686373	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686374	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686375	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686378	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686379	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686380	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686384	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686385	0.98[ASN][1000 genomes]
rs2857591	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857592	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915641	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35734276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503720	0.81[ASN][1000 genomes]
rs504677	0.94[ASN][1000 genomes]
rs531095	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7137047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs891781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121571800-121623200	Weak transcription	Colonic Mucosa	Colon
2	chr12:121583000-121634600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:121583800-121623600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr12:121583800-121634400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:121584600-121626600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:121586200-121623600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:121594200-121627600	Weak transcription	Right Ventricle	heart
8	chr12:121596200-121625600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:121596200-121629000	Weak transcription	Left Ventricle	heart
10	chr12:121596400-121634200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:121597800-121625600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr12:121602400-121634600	Weak transcription	Fetal Thymus	thymus
13	chr12:121603800-121623600	Weak transcription	Fetal Intestine Small	intestine
14	chr12:121605000-121623400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:121610800-121628800	Weak transcription	Right Atrium	heart
16	chr12:121612600-121630200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:121614000-121623000	Weak transcription	Primary B cells from cord blood	blood
18	chr12:121614000-121634600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:121614200-121624000	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:121614200-121628800	Weak transcription	Adipose Nuclei	Adipose
21	chr12:121615000-121622600	Weak transcription	Gastric	stomach
22	chr12:121615600-121623200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:121615800-121625400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:121618600-121624200	Strong transcription	Brain Hippocampus Middle	brain
25	chr12:121619200-121627400	Weak transcription	NHLF	lung
26	chr12:121619400-121624200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:121619600-121623000	Weak transcription	K562	blood
28	chr12:121620200-121626400	Strong transcription	Brain Angular Gyrus	brain
29	chr12:121620400-121624600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:121620400-121634200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr12:121621400-121624400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:121621600-121625600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:121621800-121623000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:121622000-121622800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:121622000-121622800	Enhancers	Placenta	Placenta
36	chr12:121622000-121622800	Enhancers	HMEC	breast
37	chr12:121622000-121623000	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr12:121622000-121623000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:121622000-121623000	Genic enhancers	Monocytes-CD14+_RO01746	blood
40	chr12:121622000-121623600	Strong transcription	Liver	Liver
41	chr12:121622000-121624200	Strong transcription	Ovary	ovary
42	chr12:121622000-121624800	Strong transcription	Brain Substantia Nigra	brain
43	chr12:121622000-121625600	Strong transcription	Primary T cells from cord blood	blood
44	chr12:121622200-121622600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
45	chr12:121622200-121622600	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr12:121622200-121622600	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr12:121622200-121622600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr12:121622200-121622600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:121622200-121622600	Enhancers	Esophagus	oesophagus
50	chr12:121622200-121622600	Strong transcription	Pancreas	Pancrea

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