Variant report

Variant	rs55922338
Chromosome Location	chr19:39086604-39086605
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	chr19:39086582-39086606	GM12878	blood:	n/a	n/a
2	TEAD4	chr19:39086536-39087165	K562	blood:	n/a	n/a
3	SP4	chr19:39086587-39087717	H1-hESC	embryonic stem cell:	n/a	chr19:39087555-39087571 chr19:39086880-39086896 chr19:39087534-39087550 chr19:39086916-39086932 chr19:39087143-39087154 chr19:39087178-39087194 chr19:39086758-39086774 chr19:39087176-39087192 chr19:39087532-39087548 chr19:39087303-39087319
4	POLR2A	chr19:39086443-39087600	H1-hESC	embryonic stem cell:	n/a	n/a
5	JUN	chr19:39086593-39087928	K562	blood:	n/a	chr19:39087791-39087802
6	POLR2A	chr19:39086547-39087301	K562	blood:	n/a	n/a
7	SP1	chr19:39086584-39087687	A549	lung:	n/a	chr19:39086670-39086680 chr19:39086894-39086906 chr19:39086761-39086770 chr19:39086919-39086928 chr19:39087558-39087568 chr19:39087558-39087567 chr19:39086884-39086893 chr19:39087180-39087192 chr19:39086894-39086906 chr19:39086882-39086894 chr19:39086919-39086929 chr19:39086920-39086929 chr19:39086760-39086772 chr19:39087538-39087547 chr19:39087536-39087548 chr19:39087181-39087191 chr19:39087143-39087154 chr19:39087306-39087316 chr19:39086762-39086771 chr19:39086883-39086897 chr19:39087557-39087569 chr19:39087537-39087547 chr19:39087306-39087316 chr19:39086761-39086771 chr19:39087145-39087154 chr19:39087536-39087548 chr19:39086918-39086930 chr19:39087537-39087546 chr19:39087559-39087568 chr19:39086761-39086771 chr19:39086760-39086772 chr19:39086895-39086904 chr19:39086761-39086770 chr19:39086918-39086930 chr19:39087559-39087568 chr19:39086649-39086659 chr19:39087557-39087569 chr19:39086919-39086933 chr19:39087537-39087547 chr19:39087181-39087191 chr19:39087180-39087192 chr19:39087533-39087547 chr19:39086883-39086892
8	SP1	chr19:39086598-39087735	H1-hESC	embryonic stem cell:	n/a	chr19:39086670-39086680 chr19:39086894-39086906 chr19:39086761-39086770 chr19:39086919-39086928 chr19:39087558-39087568 chr19:39087558-39087567 chr19:39086884-39086893 chr19:39087180-39087192 chr19:39086894-39086906 chr19:39086882-39086894 chr19:39086919-39086929 chr19:39086920-39086929 chr19:39086760-39086772 chr19:39087538-39087547 chr19:39087536-39087548 chr19:39087181-39087191 chr19:39087143-39087154 chr19:39087306-39087316 chr19:39086762-39086771 chr19:39086883-39086897 chr19:39087557-39087569 chr19:39087537-39087547 chr19:39087306-39087316 chr19:39086761-39086771 chr19:39087145-39087154 chr19:39087536-39087548 chr19:39086918-39086930 chr19:39087537-39087546 chr19:39087559-39087568 chr19:39086761-39086771 chr19:39086760-39086772 chr19:39086895-39086904 chr19:39086761-39086770 chr19:39086918-39086930 chr19:39087559-39087568 chr19:39086649-39086659 chr19:39087557-39087569 chr19:39086919-39086933 chr19:39087537-39087547 chr19:39087181-39087191 chr19:39087180-39087192 chr19:39087533-39087547 chr19:39086883-39086892
9	TAF1	chr19:39086592-39087090	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39086053..39087682-chr19:39099165..39101048,2	K562	blood:
2	chr19:39086098..39088583-chr19:39106611..39110096,5	K562	blood:

Variant related genes	Relation type
MAP4K1	TF binding region
ENSG00000267291	TF binding region
ENSG00000104814	Chromatin interaction
ENSG00000178982	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10404936	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10408694	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10408718	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10413936	0.80[AMR][1000 genomes]
rs12461431	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13345914	0.80[AMR][1000 genomes]
rs17847678	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1978444	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2080987	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2098657	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2098658	0.87[EUR][1000 genomes]
rs2287734	0.80[AMR][1000 genomes]
rs2287735	0.80[AMR][1000 genomes]
rs2368477	0.80[AMR][1000 genomes]
rs4802618	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73552634	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv911663	chr19:38899548-39101879	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv911665	chr19:38924814-39101879	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39053200-39086800	Weak transcription	Brain Angular Gyrus	brain
2	chr19:39053200-39086800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr19:39070600-39100000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:39074800-39087000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr19:39074800-39101600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr19:39075400-39087000	Weak transcription	Colonic Mucosa	Colon
7	chr19:39076600-39089600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr19:39076600-39093200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:39076800-39092800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr19:39077000-39101600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:39077200-39103200	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr19:39077800-39093000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:39078000-39088400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr19:39078000-39089000	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr19:39078000-39089200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr19:39078000-39089800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:39078200-39092200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:39078600-39086800	Weak transcription	Brain Hippocampus Middle	brain
19	chr19:39078800-39086800	Weak transcription	Lung	lung
20	chr19:39078800-39086800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr19:39078800-39087000	Weak transcription	Right Atrium	heart
22	chr19:39079000-39086800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr19:39079000-39086800	Weak transcription	Brain Anterior Caudate	brain
24	chr19:39081000-39088600	Strong transcription	Thymus	Thymus
25	chr19:39081400-39088400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr19:39081800-39087000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr19:39082600-39086800	Strong transcription	Primary T cells from cord blood	blood
28	chr19:39082600-39088600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr19:39083200-39086800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr19:39083400-39088600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr19:39083600-39088600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr19:39083800-39088600	Strong transcription	GM12878-XiMat	blood
33	chr19:39085000-39086800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr19:39085000-39086800	Weak transcription	Placenta	Placenta
35	chr19:39085000-39088600	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr19:39086000-39086800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr19:39086000-39088400	Strong transcription	Dnd41	blood
38	chr19:39086200-39086800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr19:39086200-39088400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
40	chr19:39086200-39088600	Strong transcription	Primary B cells from cord blood	blood
41	chr19:39086400-39086800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:39086400-39087400	Genic enhancers	Spleen	Spleen
43	chr19:39086400-39087600	Enhancers	Esophagus	oesophagus
44	chr19:39086400-39087800	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr19:39086400-39087800	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr19:39086400-39087800	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr19:39086400-39096600	Weak transcription	Fetal Thymus	thymus
48	chr19:39086400-39098400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr19:39086600-39086800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:39086600-39086800	Enhancers	Gastric	stomach

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