Variant report

Variant	rs554316503
Chromosome Location	chr3:47190661-47190662
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47189860..47191745-chr3:47198153..47199687,2	K562	blood:
2	chr3:47189967..47191564-chr3:47204385..47206673,2	MCF-7	breast:
3	chr3:47187957..47190858-chr3:47193196..47195551,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NBEAL2-2	chr3:47190262-47190757	l_2362_chr3:47180551-47192368_testes

Variant related genes	Relation type
ENSG00000181555	Chromatin interaction
ENSG00000227398	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv590210	chr3:47126543-47214122	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv590211	chr3:47189485-47256057	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47165800-47191000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:47165800-47197000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:47166000-47200800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:47166000-47201200	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:47166000-47204600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:47166200-47197200	Weak transcription	Aorta	Aorta
7	chr3:47166200-47200600	Weak transcription	Hela-S3	cervix
8	chr3:47166400-47194200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:47166600-47204200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:47167400-47202400	Weak transcription	HSMM	muscle
11	chr3:47167800-47195400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:47173600-47191000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:47175800-47200400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:47176400-47190800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:47177800-47194200	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:47178000-47190800	Weak transcription	Right Ventricle	heart
17	chr3:47178000-47194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:47181000-47193600	Weak transcription	Fetal Heart	heart
19	chr3:47182000-47192600	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr3:47182000-47195400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:47182600-47190800	Weak transcription	Small Intestine	intestine
22	chr3:47182600-47200800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:47182800-47191000	Weak transcription	Pancreas	Pancrea
24	chr3:47182800-47192000	Weak transcription	Stomach Mucosa	stomach
25	chr3:47182800-47198200	Weak transcription	Primary B cells from cord blood	blood
26	chr3:47183600-47192000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:47183600-47193800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:47183600-47200800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:47183600-47202200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:47183800-47191000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:47183800-47191000	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:47183800-47193800	Weak transcription	Primary T cells from cord blood	blood
33	chr3:47183800-47194000	Weak transcription	Dnd41	blood
34	chr3:47183800-47194200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:47183800-47194400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:47183800-47198000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:47183800-47202200	Weak transcription	NHEK	skin
38	chr3:47183800-47203000	Weak transcription	Colonic Mucosa	Colon
39	chr3:47184000-47194200	Weak transcription	Spleen	Spleen
40	chr3:47184000-47197000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:47184400-47198400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:47184600-47192200	Weak transcription	Fetal Intestine Large	intestine
43	chr3:47184600-47194200	Weak transcription	Fetal Thymus	thymus
44	chr3:47184600-47194200	Weak transcription	Psoas Muscle	Psoas
45	chr3:47184600-47198000	Weak transcription	Thymus	Thymus
46	chr3:47184600-47202200	Weak transcription	Esophagus	oesophagus
47	chr3:47184800-47194000	Weak transcription	Ovary	ovary
48	chr3:47184800-47194200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:47184800-47197000	Weak transcription	Gastric	stomach
50	chr3:47184800-47199600	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links