Variant report

Variant	rs607541
Chromosome Location	chr15:45934869-45934870
allele	G/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	NFIC	chr15:45934291-45935034	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr15:45934275-45935015	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr15:45934740-45934890	AG10803	skin:	n/a	n/a
4	STAT3	chr15:45933456-45934890	MCF10A-Er-Src	breast:	n/a	chr15:45933849-45933857 chr15:45933976-45933984 chr15:45933545-45933553
5	FOS	chr15:45932705-45934919	MCF10A-Er-Src	breast:	n/a	chr15:45933034-45933043 chr15:45933036-45933043 chr15:45933652-45933660 chr15:45933651-45933661 chr15:45933651-45933661 chr15:45933034-45933044 chr15:45933033-45933044 chr15:45933651-45933661 chr15:45933651-45933661 chr15:45933033-45933044 chr15:45933031-45933042
6	STAT3	chr15:45933454-45934929	MCF10A-Er-Src	breast:	n/a	chr15:45933849-45933857 chr15:45933976-45933984 chr15:45933545-45933553
7	FOS	chr15:45932668-45934971	MCF10A-Er-Src	breast:	n/a	chr15:45933034-45933043 chr15:45933036-45933043 chr15:45933652-45933660 chr15:45933651-45933661 chr15:45933651-45933661 chr15:45933034-45933044 chr15:45933033-45933044 chr15:45933651-45933661 chr15:45933651-45933661 chr15:45933033-45933044 chr15:45933031-45933042
8	STAT3	chr15:45932629-45934910	MCF10A-Er-Src	breast:	n/a	chr15:45933849-45933857 chr15:45933314-45933323 chr15:45933976-45933984 chr15:45933087-45933098 chr15:45933313-45933322 chr15:45933545-45933553
9	MYC	chr15:45934361-45934955	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr15:45934414-45934929	MCF10A-Er-Src	breast:	n/a	n/a
11	GATA3	chr15:45934864-45935202	T-47D	breast:	n/a	chr15:45935051-45935058 chr15:45935051-45935058 chr15:45935051-45935058
12	FOSL2	chr15:45934303-45934965	SK-N-SH	brain:	n/a	n/a
13	NFIC	chr15:45934305-45934882	SK-N-SH	brain:	n/a	n/a
14	TCF12	chr15:45934241-45934946	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:45933052..45935436-chr15:45937380..45939217,2	K562	blood:
2	chr15:45934455..45936874-chr15:45938212..45940753,2	MCF-7	breast:
3	chr15:45933273..45936098-chr15:48986463..48988127,2	MCF-7	breast:

Variant related genes	Relation type
SQRDL	TF binding region
ENSG00000137767	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1816804	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2083729	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2099880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470114	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4270120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4271550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs593126	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs607594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626808	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs629466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629880	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636910	0.80[YRI][hapmap]
rs642328	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs643190	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs644493	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs673208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs673555	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs673596	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs675413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs675876	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs675890	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs688967	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74009656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74009657	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036075	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8036651	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];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	nsv904188	chr15:45801035-45941689	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv904189	chr15:45821158-46298458	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS 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	58 gene(s)	inside rSNPs	diseases
3	nsv904190	chr15:45892672-45960897	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	n/a
4	nsv904191	chr15:45902779-46381874	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45927800-45935400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr15:45929000-45939000	Enhancers	Stomach Mucosa	stomach
3	chr15:45930000-45937800	Weak transcription	Right Ventricle	heart
4	chr15:45930200-45935800	Enhancers	Fetal Intestine Large	intestine
5	chr15:45930400-45935200	Enhancers	Colon Smooth Muscle	Colon
6	chr15:45930400-45935400	Enhancers	Fetal Intestine Small	intestine
7	chr15:45930400-45936800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:45930400-45940800	Weak transcription	Fetal Thymus	thymus
9	chr15:45930600-45940800	Weak transcription	Thymus	Thymus
10	chr15:45930800-45936800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr15:45931000-45936600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr15:45931000-45938800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr15:45931600-45936600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr15:45932200-45935200	Enhancers	HSMM	muscle
15	chr15:45932200-45935400	Enhancers	Psoas Muscle	Psoas
16	chr15:45932200-45935600	Enhancers	Pancreas	Pancrea
17	chr15:45932400-45935000	Enhancers	Duodenum Mucosa	Duodenum
18	chr15:45932400-45935000	Enhancers	HSMMtube	muscle
19	chr15:45932400-45935000	Enhancers	NH-A	brain
20	chr15:45932400-45935200	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr15:45932400-45935200	Enhancers	HUVEC	blood vessel
22	chr15:45932600-45935000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr15:45932600-45935000	Enhancers	Fetal Stomach	stomach
24	chr15:45932600-45935200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr15:45932800-45935400	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr15:45932800-45936600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr15:45933000-45935000	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr15:45933000-45935200	Enhancers	Fetal Muscle Leg	muscle
29	chr15:45933200-45936400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:45933200-45936600	Weak transcription	Primary T cells from cord blood	blood
31	chr15:45933600-45935000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:45933600-45935400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:45933600-45936000	Enhancers	HMEC	breast
34	chr15:45933800-45935000	Enhancers	Fetal Lung	lung
35	chr15:45933800-45935000	Flanking Active TSS	Hela-S3	cervix
36	chr15:45933800-45936000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:45933800-45951200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:45934000-45935400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr15:45934200-45935000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:45934200-45935000	Enhancers	Aorta	Aorta
41	chr15:45934200-45935000	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr15:45934200-45935400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr15:45934200-45936800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr15:45934200-45937200	Enhancers	Lung	lung
45	chr15:45934200-45938600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:45934200-45961600	Weak transcription	Fetal Kidney	kidney
47	chr15:45934400-45935200	Enhancers	HepG2	liver
48	chr15:45934400-45935400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:45934400-45935400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:45934400-45935400	Enhancers	Stomach Smooth Muscle	stomach

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