Variant report

Variant	rs10405152
Chromosome Location	chr19:42960172-42960173
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	JUND	chr19:42959674-42960399	HCT-116	colon:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960025-42960033
2	JUND	chr19:42959670-42960409	HCT-116	colon:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960025-42960033
3	JUND	chr19:42959799-42960345	A549	lung:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960025-42960033
4	MYC	chr19:42959814-42960285	MCF10A-Er-Src	breast:	n/a	chr19:42960024-42960033
5	KAP1	chr19:42959888-42960227	U2OS	brain:	n/a	chr19:42960023-42960032
6	FOS	chr19:42959662-42960302	MCF10A-Er-Src	breast:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960025-42960033
7	FOSL2	chr19:42959768-42960382	A549	lung:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960039-42960050 chr19:42960025-42960033 chr19:42960022-42960033
8	JUND	chr19:42959706-42960209	Hela-S3	cervix:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960025-42960033
9	FOSL2	chr19:42959824-42960283	HepG2	liver:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960039-42960050 chr19:42960025-42960033 chr19:42960022-42960033
10	FOSL1	chr19:42959604-42960394	HCT-116	colon:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960025-42960033
11	FOXA2	chr19:42959715-42960368	A549	lung:	n/a	n/a
12	NR3C1	chr19:42959769-42960177	A549	lung:	n/a	n/a
13	POLR2A	chr19:42959864-42960208	HCT-116	colon:	n/a	n/a
14	FOSL2	chr19:42959562-42960331	A549	lung:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960039-42960050 chr19:42960025-42960033 chr19:42960022-42960033
15	FOSL1	chr19:42959697-42960324	HCT-116	colon:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960025-42960033
16	MYC	chr19:42959870-42960175	MCF10A-Er-Src	breast:	n/a	chr19:42960024-42960033
17	FOSL2	chr19:42959715-42960184	MCF-7	breast:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960039-42960050 chr19:42960025-42960033 chr19:42960022-42960033
18	FOS	chr19:42959810-42960249	MCF10A-Er-Src	breast:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960025-42960033
19	STAT3	chr19:42959881-42960194	MCF10A-Er-Src	breast:	n/a	chr19:42960172-42960179
20	JUND	chr19:42959872-42960183	HepG2	liver:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960025-42960033
21	FOXA2	chr19:42959545-42960295	A549	lung:	n/a	n/a
22	FOS	chr19:42959743-42960301	MCF10A-Er-Src	breast:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960025-42960033
23	RCOR1	chr19:42959838-42960173	Hela-S3	cervix:	n/a	n/a
24	STAT3	chr19:42959766-42960338	MCF10A-Er-Src	breast:	n/a	chr19:42960172-42960179 chr19:42960219-42960227
25	JUND	chr19:42959714-42960186	HepG2	liver:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960025-42960033
26	FOSL2	chr19:42959814-42960244	HepG2	liver:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960039-42960050 chr19:42960025-42960033 chr19:42960022-42960033
27	FOS	chr19:42959837-42960212	MCF10A-Er-Src	breast:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960025-42960033
28	JUND	chr19:42959744-42960302	A549	lung:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960025-42960033
29	NR3C1	chr19:42959788-42960273	A549	lung:	n/a	n/a
30	SP1	chr19:42959667-42960451	HCT-116	colon:	n/a	chr19:42959895-42959905
31	CBX3	chr19:42959757-42960403	HCT-116	colon:	n/a	n/a
32	MYC	chr19:42960151-42960197	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42947132..42948888-chr19:42958718..42960967,2	MCF-7	breast:

Variant related genes	Relation type
LIPE-AS1	TF binding region
ENSG00000189377	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10401178	1.00[CEU][hapmap];0.82[AFR][1000 genomes]
rs10401428	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs10402853	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10403065	0.93[AMR][1000 genomes]
rs10404589	1.00[CEU][hapmap]
rs10405179	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10405410	1.00[CEU][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes]
rs10405891	0.81[AMR][1000 genomes]
rs10405942	0.93[AMR][1000 genomes]
rs10406227	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10408822	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10412074	0.82[AFR][1000 genomes]
rs10412594	0.80[AFR][1000 genomes]
rs10414396	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10414969	0.81[AMR][1000 genomes]
rs10416108	1.00[CEU][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes]
rs10416915	0.81[AMR][1000 genomes]
rs10417560	0.81[AMR][1000 genomes]
rs10418090	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10418997	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10419561	0.93[AMR][1000 genomes]
rs10422191	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423227	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10424206	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes]
rs10425666	0.82[AFR][1000 genomes]
rs11878959	1.00[CEU][hapmap]
rs11878991	1.00[CEU][hapmap]
rs11879033	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11880554	1.00[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs11881583	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882225	0.93[AMR][1000 genomes]
rs11882291	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11882701	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11883406	1.00[CEU][hapmap]
rs11883425	1.00[CEU][hapmap]
rs13343840	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13345272	0.93[AMR][1000 genomes]
rs13345659	0.81[AMR][1000 genomes]
rs16975743	0.81[AMR][1000 genomes]
rs16975750	0.81[AMR][1000 genomes]
rs16975787	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16975799	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975815	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16975862	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2051832	0.93[AMR][1000 genomes]
rs2051833	0.93[AMR][1000 genomes]
rs28403155	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28425201	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs28448880	0.81[AMR][1000 genomes]
rs28473486	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs28588100	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs28625452	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35623577	0.81[AMR][1000 genomes]
rs41348545	0.80[AFR][1000 genomes]
rs41381546	0.82[AFR][1000 genomes]
rs41421250	0.80[AFR][1000 genomes]
rs57018456	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58050143	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58162305	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58702905	1.00[EUR][1000 genomes]
rs6509015	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs6509019	1.00[CEU][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes]
rs7246161	1.00[CEU][hapmap]
rs7246591	1.00[CEU][hapmap]
rs7247278	1.00[CEU][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes]
rs7248439	0.81[AMR][1000 genomes]
rs7248907	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7249304	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7252874	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7253634	0.82[AFR][1000 genomes]
rs7255271	0.93[AMR][1000 genomes]
rs7256226	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7258854	1.00[CEU][hapmap]
rs8101378	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8104731	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8105525	1.00[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs8106836	0.81[AFR][1000 genomes]
rs8107720	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8110904	0.90[YRI][hapmap]
rs8110922	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8111171	0.81[AFR][1000 genomes]
rs9749434	0.81[AFR][1000 genomes]
rs9916999	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9917002	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42952400-42964400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:42954400-42961000	Enhancers	Primary B cells from cord blood	blood
3	chr19:42954600-42961600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:42955400-42964000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr19:42955400-42964600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr19:42955800-42966400	Weak transcription	GM12878-XiMat	blood
7	chr19:42957000-42961400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr19:42957000-42961400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr19:42957000-42966000	Weak transcription	Left Ventricle	heart
10	chr19:42957400-42964600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr19:42957400-42970600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:42958200-42960400	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr19:42959000-42960400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr19:42959000-42960400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr19:42959000-42960400	Enhancers	Fetal Intestine Large	intestine
16	chr19:42959000-42960600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:42959000-42960600	Enhancers	Duodenum Mucosa	Duodenum
18	chr19:42959000-42961600	Enhancers	Fetal Intestine Small	intestine
19	chr19:42959200-42960400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr19:42959200-42960400	Enhancers	Stomach Mucosa	stomach
21	chr19:42959200-42960600	Enhancers	HMEC	breast
22	chr19:42959200-42961000	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr19:42959400-42960200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr19:42959400-42960200	Enhancers	Fetal Lung	lung
25	chr19:42959400-42960400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:42959400-42960400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:42959400-42960400	Enhancers	HepG2	liver
28	chr19:42959400-42960400	Enhancers	NHEK	skin
29	chr19:42959400-42960800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr19:42959600-42960400	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr19:42959800-42960200	Enhancers	H9 Cell Line	embryonic stem cell
32	chr19:42959800-42960200	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr19:42959800-42960200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr19:42959800-42960200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:42959800-42960200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
36	chr19:42959800-42960200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:42959800-42960200	Flanking Active TSS	A549	lung
38	chr19:42959800-42960200	Enhancers	HSMM	muscle
39	chr19:42959800-42960200	Enhancers	HSMMtube	muscle
40	chr19:42959800-42960200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr19:42959800-42960400	Enhancers	Primary B cells from peripheral blood	blood
42	chr19:42959800-42960400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:42959800-42960400	Enhancers	Adipose Nuclei	Adipose
44	chr19:42959800-42960400	Enhancers	Right Atrium	heart
45	chr19:42960000-42960200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:42960000-42960200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:42960000-42960200	Enhancers	Colonic Mucosa	Colon
48	chr19:42960000-42960200	Enhancers	Placenta	Placenta
49	chr19:42960000-42960200	Enhancers	Lung	lung
50	chr19:42960000-42960200	Enhancers	Placenta Amnion	Placenta Amnion

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