Variant report

Variant	rs7245385
Chromosome Location	chr19:42947412-42947413
allele	A/G
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	E2F6	chr19:42946928-42947485	H1-hESC	embryonic stem cell:	n/a	chr19:42947300-42947307 chr19:42947300-42947307 chr19:42947299-42947311 chr19:42947300-42947307
2	FOS	chr19:42946902-42947446	MCF10A-Er-Src	breast:	n/a	chr19:42947063-42947070 chr19:42947063-42947071 chr19:42947062-42947072 chr19:42947063-42947071
3	STAT3	chr19:42947017-42947450	MCF10A-Er-Src	breast:	n/a	chr19:42947190-42947198 chr19:42947188-42947199
4	STAT3	chr19:42947017-42947427	MCF10A-Er-Src	breast:	n/a	chr19:42947190-42947198 chr19:42947188-42947199
5	MAX	chr19:42947087-42947455	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr19:42946983-42947505	MCF-7	breast:	n/a	chr19:42947063-42947072
7	STAT3	chr19:42946921-42947488	MCF10A-Er-Src	breast:	n/a	chr19:42947190-42947198 chr19:42947188-42947199
8	E2F4	chr19:42947124-42947455	MCF10A-Er-Src	breast:	n/a	chr19:42947300-42947307 chr19:42947300-42947307 chr19:42947299-42947311 chr19:42947300-42947307

Variant related genes	Relation type
CXCL17	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10402245	0.92[ASW][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs10405410	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10405891	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411253	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10413332	0.87[YRI][hapmap]
rs10414969	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416062	0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416915	0.92[AMR][1000 genomes]
rs10417560	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422000	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10423047	0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10423136	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10425139	0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11880554	1.00[TSI][hapmap]
rs13345659	1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975743	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975750	1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975751	0.89[YRI][hapmap]
rs16975799	1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap]
rs17340417	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28448880	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28514561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35623577	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6509015	1.00[TSI][hapmap]
rs6509019	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7248439	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7251638	0.86[ASW][hapmap];0.89[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7252470	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7254369	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7254839	0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7255015	0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73556352	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73556356	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8100511	0.91[YRI][hapmap]
rs8102976	0.86[ASW][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8103051	0.92[YRI][hapmap]
rs8103108	0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8105525	1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42938000-42950200	Weak transcription	Gastric	stomach
2	chr19:42938000-42954200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr19:42944600-42947600	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr19:42945200-42948200	Weak transcription	Small Intestine	intestine
5	chr19:42945400-42948000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:42945400-42948200	Weak transcription	Colonic Mucosa	Colon
7	chr19:42945600-42948000	Enhancers	HepG2	liver
8	chr19:42945600-42948200	Weak transcription	Spleen	Spleen
9	chr19:42945800-42948200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr19:42945800-42950200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr19:42946000-42948200	Weak transcription	Fetal Lung	lung
12	chr19:42946200-42953600	Weak transcription	Adipose Nuclei	Adipose
13	chr19:42946400-42949000	Enhancers	Fetal Intestine Large	intestine
14	chr19:42946600-42947600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr19:42946800-42947600	Enhancers	Placenta Amnion	Placenta Amnion
16	chr19:42946800-42948600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:42946800-42949000	Enhancers	Fetal Intestine Small	intestine
18	chr19:42946800-42949000	Enhancers	A549	lung
19	chr19:42946800-42949200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:42947000-42948200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr19:42947000-42948600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr19:42947000-42949000	Enhancers	Liver	Liver
23	chr19:42947000-42952800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr19:42947000-42952800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr19:42947000-42952800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr19:42947200-42948000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr19:42947200-42948200	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr19:42947200-42948200	Weak transcription	Pancreas	Pancrea
29	chr19:42947200-42948400	Weak transcription	Esophagus	oesophagus
30	chr19:42947200-42950200	Weak transcription	Lung	lung
31	chr19:42947200-42950400	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr19:42947200-42952200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:42947200-42953200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr19:42947200-42954400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr19:42947200-42954400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr19:42947200-42954400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:42947400-42947600	Flanking Active TSS	Stomach Mucosa	stomach
38	chr19:42947400-42949000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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