Variant report

Variant	rs11609399
Chromosome Location	chr12:48501161-48501162
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCLAF1	chr12:48500934-48501330	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:48498887-48501339	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:48498962-48501361	Raji	blood:	n/a	n/a
4	FOXA1	chr12:48501148-48501506	HepG2	liver:	n/a	n/a
5	TAF1	chr12:48501015-48501408	GM12878	blood:	n/a	n/a
6	PAX5	chr12:48500920-48501319	GM12891	blood:	n/a	n/a
7	HCFC1	chr12:48498126-48501600	Hela-S3	cervix:	n/a	n/a
8	PAX5	chr12:48500966-48501287	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:48498418-48501460	GM18505	blood:	n/a	n/a
10	EBF1	chr12:48501069-48501319	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:48498937-48501364	GM12878	blood:	n/a	n/a
12	PAX5	chr12:48500978-48501340	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:48498334-48501462	GM12891	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48492914..48496557-chr12:48498180..48501677,4	MCF-7	breast:
2	chr12:48496939..48501728-chr12:48549612..48553634,6	MCF-7	breast:
3	chr12:48498567..48501846-chr12:48512929..48518601,8	MCF-7	breast:
4	chr12:48500571..48503072-chr12:48556879..48559027,2	K562	blood:
5	chr12:48500761..48502432-chr12:48514527..48516446,2	MCF-7	breast:
6	chr12:48497586..48502171-chr12:48511099..48514258,8	MCF-7	breast:
7	chr12:48499494..48502600-chr12:48549917..48552067,4	MCF-7	breast:
8	chr12:48495831..48503326-chr12:48548997..48555180,8	K562	blood:
9	chr12:48497262..48501671-chr12:48511273..48513832,5	K562	blood:

No data

Variant related genes	Relation type
SENP1	TF binding region
ENSG00000177981	Chromatin interaction
ENSG00000152556	Chromatin interaction
ENSG00000258051	Chromatin interaction
ENSG00000079387	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1018973	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs10492080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783230	0.94[ASN][1000 genomes]
rs10783231	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10783232	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10875751	0.90[ASN][1000 genomes]
rs11168451	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11168455	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11612578	0.88[CEU][hapmap];0.96[JPT][hapmap]
rs11612970	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11613485	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11613781	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12580764	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12581972	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12822085	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1476608	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1489111	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs17122565	0.95[JPT][hapmap]
rs17122611	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17122612	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17122613	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17122651	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1859441	0.86[CEU][hapmap];0.86[YRI][hapmap];0.80[EUR][1000 genomes]
rs1968071	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2258342	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2634699	0.82[CHB][hapmap]
rs2732455	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2732477	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2732487	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs3742074	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4075913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4141065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4293182	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4589362	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4760611	0.86[CEU][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs4760614	0.83[EUR][1000 genomes]
rs4760615	0.81[EUR][1000 genomes]
rs4760620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4760677	0.83[EUR][1000 genomes]
rs4760683	0.87[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4760685	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4760692	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4760698	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs57054831	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57380031	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57655233	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58046797	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58331734	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59766465	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60567660	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60681522	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6580651	0.83[EUR][1000 genomes]
rs6580653	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6580656	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6580660	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7133249	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs726354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72644842	0.83[EUR][1000 genomes]
rs72644843	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72644844	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72644845	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72644846	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72644847	0.98[EUR][1000 genomes]
rs7296913	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7305418	0.85[CEU][hapmap]
rs7310579	0.81[EUR][1000 genomes]
rs7312326	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7315258	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7485057	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7485824	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs757556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7957764	0.81[EUR][1000 genomes]
rs7959755	0.94[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs7963934	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7967762	0.80[CEU][hapmap]
rs7969749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7971668	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs879242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs901964	0.86[CHB][hapmap];0.81[JPT][hapmap]

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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11609399	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48500200-48501200	Enhancers	Spleen	Spleen
2	chr12:48500400-48502000	Flanking Active TSS	GM12878-XiMat	blood
3	chr12:48500600-48501200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:48500600-48501200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:48500600-48501200	Enhancers	Primary hematopoietic stem cells	blood
6	chr12:48500600-48501200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:48500600-48501200	Enhancers	Fetal Lung	lung
8	chr12:48500600-48501200	Enhancers	Small Intestine	intestine
9	chr12:48500600-48501400	Enhancers	Primary B cells from peripheral blood	blood
10	chr12:48500600-48501400	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr12:48500600-48501400	Enhancers	Fetal Heart	heart
12	chr12:48500600-48501600	Enhancers	Fetal Intestine Large	intestine
13	chr12:48500800-48501200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:48500800-48501200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr12:48500800-48501200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr12:48500800-48501200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr12:48500800-48501200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr12:48500800-48501200	Enhancers	Duodenum Mucosa	Duodenum
19	chr12:48500800-48501200	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr12:48500800-48501200	Enhancers	HMEC	breast
21	chr12:48500800-48501200	Enhancers	NHDF-Ad	bronchial
22	chr12:48500800-48501200	Enhancers	NHLF	lung
23	chr12:48500800-48501400	Enhancers	Primary T cells fromperipheralblood	blood
24	chr12:48500800-48501400	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr12:48500800-48501400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:48500800-48501400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr12:48500800-48501400	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr12:48500800-48501400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:48500800-48501400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:48500800-48501400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr12:48500800-48501400	Enhancers	Fetal Kidney	kidney
32	chr12:48500800-48501400	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr12:48500800-48501400	Enhancers	NHEK	skin
34	chr12:48500800-48501600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:48500800-48501600	Enhancers	Fetal Intestine Small	intestine
36	chr12:48500800-48502000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:48500800-48502200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:48500800-48502200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:48501000-48501200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:48501000-48501200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:48501000-48501200	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr12:48501000-48501200	Enhancers	Hela-S3	cervix
43	chr12:48501000-48501400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:48501000-48501400	Enhancers	Dnd41	blood
45	chr12:48501000-48501400	Enhancers	HUVEC	blood vessel
46	chr12:48501000-48501600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr12:48501000-48501800	Enhancers	Primary T cells from cord blood	blood
48	chr12:48501000-48501800	Enhancers	HepG2	liver
49	chr12:48501000-48503600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:48501000-48504000	Weak transcription	Psoas Muscle	Psoas

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