Variant report

Variant	rs35623577
Chromosome Location	chr19:42910923-42910924
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	POLR2A	chr19:42910607-42910980	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42900679..42903538-chr19:42909669..42912049,2	K562	blood:
2	chr19:42901013..42903466-chr19:42908156..42911805,3	MCF-7	breast:
3	chr19:42904315..42908218-chr19:42909528..42916555,10	K562	blood:

Variant related genes	Relation type
LIPE	TF binding region
ENSG00000213904	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10405152	0.81[AMR][1000 genomes]
rs10405891	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411253	1.00[EUR][1000 genomes]
rs10414969	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416062	1.00[EUR][1000 genomes]
rs10416915	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10417560	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10418997	0.81[AMR][1000 genomes]
rs10422000	1.00[EUR][1000 genomes]
rs10422191	0.81[AMR][1000 genomes]
rs10423047	1.00[EUR][1000 genomes]
rs10423136	1.00[EUR][1000 genomes]
rs10425139	1.00[EUR][1000 genomes]
rs11882701	0.81[AMR][1000 genomes]
rs13343840	0.81[AMR][1000 genomes]
rs13345659	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975743	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975750	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975799	0.81[AMR][1000 genomes]
rs16975862	0.81[AMR][1000 genomes]
rs17340417	0.92[AMR][1000 genomes]
rs28448880	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28514561	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28625452	0.81[AMR][1000 genomes]
rs7245385	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248439	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7251638	1.00[EUR][1000 genomes]
rs7252470	1.00[EUR][1000 genomes]
rs7254369	0.92[AMR][1000 genomes]
rs7254839	1.00[EUR][1000 genomes]
rs7255015	1.00[EUR][1000 genomes]
rs73556352	1.00[EUR][1000 genomes]
rs73556356	1.00[EUR][1000 genomes]
rs8102976	1.00[EUR][1000 genomes]
rs8103108	1.00[EUR][1000 genomes]
rs8104731	0.81[AMR][1000 genomes]
rs9917002	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
7	nsv911788	chr19:42887492-42930652	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv911792	chr19:42901430-42929254	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv911793	chr19:42901430-42929502	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv911794	chr19:42901430-42930652	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv911795	chr19:42901430-42932699	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv579632	chr19:42904653-42912403	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
13	nsv911798	chr19:42904653-42930652	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv911799	chr19:42905645-42930652	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv911800	chr19:42906914-42930652	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv911801	chr19:42910416-42929502	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42906200-42911000	Weak transcription	Gastric	stomach
2	chr19:42906200-42926200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr19:42906400-42913200	Weak transcription	HSMMtube	muscle
4	chr19:42906400-42913600	Weak transcription	Psoas Muscle	Psoas
5	chr19:42906400-42913600	Weak transcription	Stomach Mucosa	stomach
6	chr19:42906400-42913600	Weak transcription	HSMM	muscle
7	chr19:42906400-42915800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr19:42906400-42916200	Weak transcription	HMEC	breast
9	chr19:42906400-42924400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr19:42906400-42926400	Weak transcription	Colonic Mucosa	Colon
11	chr19:42906600-42911000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:42906600-42911400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:42906600-42913600	Weak transcription	Colon Smooth Muscle	Colon
14	chr19:42906600-42918600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr19:42906600-42926400	Weak transcription	Fetal Lung	lung
16	chr19:42906800-42913600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr19:42906800-42916600	Strong transcription	Fetal Intestine Small	intestine
18	chr19:42906800-42916800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr19:42906800-42923200	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr19:42906800-42924000	Weak transcription	A549	lung
21	chr19:42906800-42924400	Weak transcription	Osteobl	bone
22	chr19:42906800-42925200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr19:42907000-42911200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr19:42907000-42912400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:42907000-42912800	Strong transcription	Primary T cells from cord blood	blood
26	chr19:42907000-42914000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr19:42907000-42916400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:42907000-42924200	Strong transcription	Fetal Stomach	stomach
29	chr19:42907000-42924400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:42907200-42912400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr19:42907200-42912800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:42907200-42913200	Strong transcription	Spleen	Spleen
33	chr19:42907200-42913600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr19:42907200-42913600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr19:42907200-42915200	Strong transcription	Fetal Thymus	thymus
36	chr19:42907200-42916200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:42907400-42911800	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr19:42907400-42912200	Strong transcription	Brain Cingulate Gyrus	brain
39	chr19:42907400-42912800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:42907400-42913000	Weak transcription	Pancreas	Pancrea
41	chr19:42907400-42926600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:42907600-42912600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:42907600-42916400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr19:42907800-42912400	Strong transcription	Brain Substantia Nigra	brain
45	chr19:42907800-42915200	Strong transcription	Thymus	Thymus
46	chr19:42908600-42912400	Strong transcription	Brain Angular Gyrus	brain
47	chr19:42908600-42912400	Strong transcription	Brain Anterior Caudate	brain
48	chr19:42908600-42912800	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr19:42908800-42911400	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr19:42908800-42911600	Strong transcription	Primary T helper cells PMA-I stimulated	--

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