Variant report

Variant	rs2003098
Chromosome Location	chr19:44114459-44114460
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	RCOR1	chr19:44114176-44114684	K562	blood:	n/a	n/a
2	POLR2A	chr19:44114320-44114498	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44109603..44114689-chr19:44115292..44119073,6	K562	blood:
2	chr19:44112456..44114757-chr2:168997248..168998766,2	MCF-7	breast:
3	chr19:44098915..44102164-chr19:44112167..44115504,5	K562	blood:

Variant related genes	Relation type
SRRM5	TF binding region
ENSG00000124444	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000226763	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11083712	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11671645	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12461175	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1402325	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1402326	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17655574	0.86[EUR][1000 genomes]
rs1879387	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2079646	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2302421	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3746002	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3746003	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3815422	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803643	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4803644	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73038867	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs767540	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs880108	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][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	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv833839	chr19:44099813-44272299	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44101800-44123200	Weak transcription	Small Intestine	intestine
2	chr19:44102000-44122600	Weak transcription	Fetal Kidney	kidney
3	chr19:44102200-44114600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr19:44102200-44122600	Weak transcription	Psoas Muscle	Psoas
5	chr19:44102400-44119600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:44102400-44122600	Weak transcription	NHDF-Ad	bronchial
7	chr19:44102600-44115800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr19:44102600-44116200	Weak transcription	Hela-S3	cervix
9	chr19:44102600-44120600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:44102600-44121200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:44102600-44122600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr19:44102600-44122600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr19:44102800-44120000	Strong transcription	Fetal Stomach	stomach
14	chr19:44103200-44115000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr19:44104000-44116000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr19:44104000-44116200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:44104400-44122800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr19:44104600-44115800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr19:44104600-44116200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr19:44104600-44116400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr19:44104800-44123000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr19:44105200-44115800	Weak transcription	HSMM	muscle
23	chr19:44105800-44116200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr19:44106000-44120000	Weak transcription	Right Atrium	heart
25	chr19:44106000-44122600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr19:44106200-44116000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr19:44106200-44122800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr19:44106400-44116000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr19:44106800-44115800	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr19:44107000-44115800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:44107200-44114800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:44107200-44116400	Weak transcription	Ovary	ovary
33	chr19:44107200-44116600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr19:44107400-44115800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr19:44107400-44116200	Weak transcription	Fetal Intestine Large	intestine
36	chr19:44109400-44118800	Strong transcription	Dnd41	blood
37	chr19:44110600-44119800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr19:44111200-44116000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr19:44111400-44115000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr19:44111400-44116000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:44111400-44116000	Weak transcription	Brain Angular Gyrus	brain
42	chr19:44111600-44115800	Weak transcription	HepG2	liver
43	chr19:44111600-44116200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:44111600-44120400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr19:44111800-44115800	Weak transcription	GM12878-XiMat	blood
46	chr19:44111800-44116000	Weak transcription	NHEK	skin
47	chr19:44112000-44118600	Strong transcription	Thymus	Thymus
48	chr19:44112000-44119200	Strong transcription	Fetal Muscle Leg	muscle
49	chr19:44112000-44122600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr19:44112200-44114800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links