Variant report

Variant	rs855630
Chromosome Location	chr19:38602662-38602663
allele	A/C
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	CTCF	chr19:38602650-38602785	GM12891	blood:	n/a	n/a
2	MYC	chr19:38602542-38602905	MCF-7	breast:	n/a	chr19:38602848-38602858
3	POLR2A	chr19:38602436-38602988	A549	lung:	n/a	n/a
4	SUZ12	chr19:38602468-38602986	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr19:38602044-38603123	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:38602392-38602941	A549	lung:	n/a	n/a
7	POLR2A	chr19:38602515-38602784	Gliobla	brain:	n/a	n/a
8	POLR2A	chr19:38602277-38602943	MCF-7	breast:	n/a	n/a
9	MAX	chr19:38602512-38602993	NB4	blood:	n/a	chr19:38602899-38602909 chr19:38602848-38602858
10	POLR2A	chr19:38602194-38602934	GM12878	blood:	n/a	n/a
11	MAX	chr19:38602384-38602991	HUVEC	blood vessel:	n/a	chr19:38602899-38602909 chr19:38602848-38602858
12	POLR2A	chr19:38602595-38602783	GM12878	blood:	n/a	n/a
13	BCL3	chr19:38602389-38602782	GM12878	blood:	n/a	n/a
14	NR2C2	chr19:38602496-38603008	GM12878	blood:	n/a	n/a
15	ZBTB33	chr19:38602405-38602941	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:38602397-38602827	MCF-7	breast:	n/a	n/a
17	MYC	chr19:38602491-38602800	MCF-7	breast:	n/a	n/a
18	POLR2A	chr19:38602447-38602910	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:38602293-38602948	A549	lung:	n/a	n/a
20	POLR2A	chr19:38602434-38602970	GM12878	blood:	n/a	n/a
21	BCL3	chr19:38602486-38602862	GM12878	blood:	n/a	n/a
22	MYC	chr19:38602479-38602810	MCF-7	breast:	n/a	n/a
23	POLR2A	chr19:38602453-38602948	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr19:38602492-38602913	GM19239	blood:	n/a	n/a
25	POLR2A	chr19:38602255-38603067	GM12892	blood:	n/a	n/a
26	POLR2A	chr19:38602463-38602874	HepG2	liver:	n/a	n/a
27	MYC	chr19:38602483-38602839	MCF-7	breast:	n/a	n/a
28	CTCF	chr19:38602557-38602733	MCF-7	breast:	n/a	n/a
29	POLR2A	chr19:38602545-38602823	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38396450..38399349-chr19:38602232..38604723,2	K562	blood:

Variant related genes	Relation type
ENSG00000268764	TF binding region
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10403716	0.86[EUR][1000 genomes]
rs10405667	0.91[EUR][1000 genomes]
rs10422665	0.81[EUR][1000 genomes]
rs1568975	0.91[EUR][1000 genomes]
rs1614979	0.92[EUR][1000 genomes]
rs1622409	0.92[EUR][1000 genomes]
rs1625884	0.95[EUR][1000 genomes]
rs1654355	0.91[EUR][1000 genomes]
rs1654357	0.92[EUR][1000 genomes]
rs1654358	0.92[EUR][1000 genomes]
rs1654359	0.92[EUR][1000 genomes]
rs1654365	0.95[EUR][1000 genomes]
rs1654367	0.91[EUR][1000 genomes]
rs1725461	0.90[EUR][1000 genomes]
rs1725473	0.94[EUR][1000 genomes]
rs1725479	0.92[EUR][1000 genomes]
rs1725512	0.87[EUR][1000 genomes]
rs2005054	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2082442	0.86[EUR][1000 genomes]
rs2082443	0.86[EUR][1000 genomes]
rs28412601	0.83[EUR][1000 genomes]
rs28581256	0.90[EUR][1000 genomes]
rs3760882	0.95[EUR][1000 genomes]
rs3810356	0.95[EUR][1000 genomes]
rs4802233	0.92[EUR][1000 genomes]
rs4802239	0.95[EUR][1000 genomes]
rs4802247	0.90[EUR][1000 genomes]
rs4803786	0.91[EUR][1000 genomes]
rs4803800	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803801	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803802	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803803	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803809	0.86[EUR][1000 genomes]
rs4803810	0.86[EUR][1000 genomes]
rs56166457	0.96[EUR][1000 genomes]
rs56293547	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58152231	0.92[EUR][1000 genomes]
rs59185302	0.91[EUR][1000 genomes]
rs59579475	0.96[EUR][1000 genomes]
rs59924887	0.91[EUR][1000 genomes]
rs61388128	0.91[EUR][1000 genomes]
rs705505	0.92[EUR][1000 genomes]
rs71179415	0.85[EUR][1000 genomes]
rs7248428	0.81[EUR][1000 genomes]
rs7250034	0.86[EUR][1000 genomes]
rs729625	0.91[EUR][1000 genomes]
rs729626	0.92[EUR][1000 genomes]
rs735615	0.92[EUR][1000 genomes]
rs754123	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8105468	0.91[EUR][1000 genomes]
rs8106266	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs855603	0.81[EUR][1000 genomes]
rs855619	0.92[EUR][1000 genomes]
rs855621	0.92[EUR][1000 genomes]
rs855623	0.92[EUR][1000 genomes]
rs855624	0.92[EUR][1000 genomes]
rs855625	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855627	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs855631	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs855633	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855634	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855638	0.92[EUR][1000 genomes]
rs855640	0.92[EUR][1000 genomes]
rs855641	0.95[EUR][1000 genomes]
rs860623	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs863020	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs941039	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs941040	0.92[EUR][1000 genomes]
rs9941456	0.86[EUR][1000 genomes]
rs9941467	0.88[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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	esv3403741	chr19:38600512-38604910	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:38567600-38605400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:38573600-38610000	Strong transcription	Fetal Intestine Large	intestine
4	chr19:38581600-38610000	Weak transcription	Psoas Muscle	Psoas
5	chr19:38587000-38605400	Strong transcription	Primary B cells from peripheral blood	blood
6	chr19:38587200-38603200	Strong transcription	Primary B cells from cord blood	blood
7	chr19:38587200-38613600	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr19:38587400-38613400	Strong transcription	Duodenum Mucosa	Duodenum
9	chr19:38588600-38604000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:38588800-38606600	Strong transcription	Liver	Liver
11	chr19:38589200-38606800	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr19:38590200-38605200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:38590200-38605800	Strong transcription	Adipose Nuclei	Adipose
14	chr19:38590200-38606600	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr19:38590200-38606600	Strong transcription	Stomach Smooth Muscle	stomach
16	chr19:38590200-38611000	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr19:38590400-38606400	Strong transcription	Fetal Brain Female	brain
18	chr19:38590400-38609800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr19:38590800-38602800	Strong transcription	Spleen	Spleen
20	chr19:38590800-38603600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr19:38590800-38603800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr19:38590800-38606600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:38590800-38608800	Strong transcription	Fetal Intestine Small	intestine
24	chr19:38591000-38605000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:38591200-38605400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr19:38591200-38605400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:38591200-38605800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr19:38591400-38603600	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr19:38591400-38605400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr19:38591800-38609000	Strong transcription	Fetal Stomach	stomach
31	chr19:38591800-38642800	Weak transcription	Small Intestine	intestine
32	chr19:38594400-38606800	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr19:38594600-38606800	Strong transcription	GM12878-XiMat	blood
34	chr19:38594800-38603000	Strong transcription	Primary T cells from cord blood	blood
35	chr19:38595400-38603600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr19:38595800-38603000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:38595800-38605000	Strong transcription	Fetal Muscle Trunk	muscle
38	chr19:38595800-38605800	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr19:38595800-38606200	Strong transcription	Ovary	ovary
40	chr19:38595800-38606600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:38596000-38603000	Strong transcription	Brain Anterior Caudate	brain
42	chr19:38596000-38603000	Strong transcription	Rectal Smooth Muscle	rectum
43	chr19:38596000-38603000	Strong transcription	Dnd41	blood
44	chr19:38596000-38603200	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr19:38596000-38603200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr19:38596000-38604200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr19:38596000-38610000	Strong transcription	Fetal Muscle Leg	muscle
48	chr19:38596000-38613800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:38596200-38603000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr19:38596200-38603200	Strong transcription	Primary hematopoietic stem cells	blood

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