Variant report

Variant	rs542739896
Chromosome Location	chr3:150125011-150125012
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	chr3:150125006-150126595	SK-N-MC	brain:	n/a	n/a
2	RCOR1	chr3:150124635-150128185	K562	blood:	n/a	n/a
3	POLR2A	chr3:150124962-150128050	U87	brain:	n/a	n/a
4	POLR2A	chr3:150124821-150129086	SK-N-MC	brain:	n/a	n/a
5	JUN	chr3:150124199-150130937	K562	blood:	n/a	chr3:150126610-150126621 chr3:150126364-150126373 chr3:150126007-150126016 chr3:150126003-150126016 chr3:150125540-150125551 chr3:150125537-150125549 chr3:150130480-150130492 chr3:150127088-150127099
6	JUND	chr3:150124952-150126987	K562	blood:	n/a	chr3:150126610-150126621 chr3:150126364-150126373 chr3:150126007-150126016 chr3:150125540-150125551 chr3:150125537-150125549
7	POLR2A	chr3:150124997-150127275	SK-N-SH	brain:	n/a	n/a
8	JUND	chr3:150124892-150128974	SK-N-SH	brain:	n/a	chr3:150126610-150126621 chr3:150126364-150126373 chr3:150126007-150126016 chr3:150125540-150125551 chr3:150125537-150125549 chr3:150127088-150127099
9	POLR2A	chr3:150124952-150127237	HUVEC	blood vessel:	n/a	n/a
10	HCFC1	chr3:150124974-150130064	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:150124838-150130078	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr3:150124968-150128045	U87	brain:	n/a	n/a
13	POLR2A	chr3:150124964-150127292	HUVEC	blood vessel:	n/a	n/a
14	CHD1	chr3:150124409-150133231	IMR90	lung:	n/a	chr3:150126810-150126820
15	POLR2A	chr3:150124627-150127052	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr3:150124973-150129691	HUVEC	blood vessel:	n/a	n/a
17	IRF1	chr3:150124923-150126793	K562	blood:	n/a	chr3:150126197-150126211 chr3:150125938-150125952 chr3:150126193-150126213 chr3:150125994-150126008 chr3:150126201-150126211 chr3:150125176-150125187 chr3:150126200-150126213 chr3:150126200-150126213 chr3:150126200-150126213
18	MYC	chr3:150125008-150127265	K562	blood:	n/a	chr3:150125747-150125757
19	POLR2A	chr3:150124919-150127364	GM12891	blood:	n/a	n/a
20	POLR2A	chr3:150124872-150128185	IMR90	lung:	n/a	n/a
21	RELA	chr3:150124998-150127137	GM19099	blood:	n/a	n/a
22	EP300	chr3:150124785-150126900	K562	blood:	n/a	chr3:150126363-150126372 chr3:150126547-150126563 chr3:150126546-150126562 chr3:150126310-150126319 chr3:150126301-150126317 chr3:150126553-150126569
23	ARID3A	chr3:150124301-150126226	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:149953695..149960076-chr3:150124777..150129995,22	MCF-7	breast:
2	chr3:150122822..150130151-chr3:150261910..150267967,8	K562	blood:
3	chr3:150124697..150131961-chr3:150259924..150266159,12	MCF-7	breast:
4	chr3:150124105..150129008-chr3:150174357..150179992,6	MCF-7	breast:
5	chr3:150116751..150119532-chr3:150121582..150125856,6	K562	blood:
6	chr3:150121790..150130149-chr3:150138506..150143439,10	MCF-7	breast:
7	chr19:55917718..55920668-chr3:150122792..150125732,2	K562	blood:
8	chr3:150105305..150107998-chr3:150123098..150125972,3	K562	blood:
9	chr3:150124642..150128245-chr3:150263775..150265951,4	K562	blood:
10	chr3:150101805..150104730-chr3:150121434..150125041,3	K562	blood:
11	chr3:150003129..150006271-chr3:150124947..150129304,6	MCF-7	breast:
12	chr1:1617816..1618735-chr3:150124965..150125497,2	Hela-S3	cervix:
13	chr3:149953873..149961412-chr3:150123750..150131229,19	MCF-7	breast:
14	chr3:150124887..150127352-chr3:150262732..150264840,2	MCF-7	breast:

Variant related genes	Relation type
TSC22D2	TF binding region
ENSG00000196428	Chromatin interaction
ENSG00000243550	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000120742	Chromatin interaction
ENSG00000144895	Chromatin interaction
ENSG00000244541	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829755	chr3:149992023-150156001	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	esv1828464	chr3:150096071-150149868	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv877645	chr3:150103135-150212698	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1818335	chr3:150122121-150128717	Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	esv14316	chr3:150124574-150128485	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150121600-150125200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:150122200-150125200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:150123600-150125200	Enhancers	Placenta Amnion	Placenta Amnion
4	chr3:150124400-150125200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:150124600-150125200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
6	chr3:150124600-150125200	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:150124600-150125200	Flanking Active TSS	HUVEC	blood vessel
8	chr3:150124600-150125200	Flanking Active TSS	NHDF-Ad	bronchial
9	chr3:150124600-150125200	Flanking Active TSS	Osteobl	bone
10	chr3:150124600-150125400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:150124600-150126200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:150124600-150127000	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr3:150124600-150127400	Active TSS	NHLF	lung
14	chr3:150124600-150130600	Active TSS	Aorta	Aorta
15	chr3:150124600-150132200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:150124600-150133000	Active TSS	Fetal Kidney	kidney
17	chr3:150124600-150133000	Active TSS	Right Atrium	heart
18	chr3:150124800-150125200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:150124800-150125200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr3:150124800-150125200	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr3:150124800-150125200	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr3:150124800-150125200	Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr3:150124800-150125200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:150124800-150125400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr3:150124800-150125400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:150124800-150125400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr3:150124800-150125400	Flanking Active TSS	Fetal Heart	heart
28	chr3:150124800-150125400	Flanking Active TSS	HMEC	breast
29	chr3:150124800-150125400	Flanking Active TSS	NHEK	skin
30	chr3:150124800-150125600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:150124800-150125800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:150124800-150126400	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr3:150124800-150128600	Active TSS	HSMM	muscle
34	chr3:150124800-150128800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:150124800-150129200	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr3:150124800-150133600	Active TSS	Stomach Smooth Muscle	stomach
37	chr3:150125000-150125200	Enhancers	H1 Cell Line	embryonic stem cell
38	chr3:150125000-150125200	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr3:150125000-150125200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:150125000-150125200	Enhancers	Primary B cells from peripheral blood	blood
41	chr3:150125000-150125200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:150125000-150125200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:150125000-150125200	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr3:150125000-150125200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:150125000-150125200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr3:150125000-150125200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:150125000-150125200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:150125000-150125200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:150125000-150125200	Flanking Active TSS	Colon Smooth Muscle	Colon
50	chr3:150125000-150125200	Active TSS	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links