Variant report

Variant	rs200622561
Chromosome Location	chr1:227922413-227922414
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	chr1:227922095-227923743	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr1:227922324-227923419	K562	blood:	n/a	n/a
3	TCF12	chr1:227922345-227923575	A549	lung:	n/a	chr1:227922625-227922635
4	MAX	chr1:227922265-227923415	MCF-7	breast:	n/a	chr1:227922598-227922607
5	POLR2A	chr1:227922205-227924256	PBDE	blood:	n/a	n/a
6	SIN3AK20	chr1:227922266-227923575	K562	blood:	n/a	n/a
7	MYC	chr1:227922282-227923383	NB4	blood:	n/a	chr1:227922598-227922607
8	MAZ	chr1:227922175-227924196	IMR90	lung:	n/a	chr1:227922598-227922607
9	CTCF	chr1:227922300-227922450	HCPEpiC	choroid plexus:	n/a	n/a
10	POLR2A	chr1:227922135-227923848	HepG2	liver:	n/a	n/a
11	MAX	chr1:227922166-227923527	A549	lung:	n/a	chr1:227922598-227922607
12	POLR2A	chr1:227921936-227924227	MCF10A-Er-Src	breast:	n/a	n/a
13	REST	chr1:227922234-227923744	H1-neurons	neurons:	n/a	chr1:227922319-227922339
14	POLR2A	chr1:227922334-227923568	GM19099	blood:	n/a	n/a
15	POLR2A	chr1:227922323-227923444	GM12892	blood:	n/a	n/a
16	HCFC1	chr1:227922209-227923627	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:227922298-227923555	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:227922370-227923611	GM18951	blood:	n/a	n/a
19	TAF1	chr1:227922391-227923413	HepG2	liver:	n/a	n/a
20	POLR2A	chr1:227922180-227923715	GM12892	blood:	n/a	n/a
21	MXI1	chr1:227921582-227923837	IMR90	lung:	n/a	n/a
22	POLR2A	chr1:227922290-227923402	HepG2	liver:	n/a	n/a
23	POLR2A	chr1:227921962-227923649	PFSK-1	brain:	n/a	n/a
24	MYC	chr1:227922283-227923324	K562	blood:	n/a	chr1:227922598-227922607
25	POLR2A	chr1:227922317-227923605	GM18505	blood:	n/a	n/a
26	KAP1	chr1:227922380-227923230	HEK293	kidney:	n/a	n/a
27	POLR2A	chr1:227922244-227923694	GM19193	blood:	n/a	n/a
28	POLR2A	chr1:227922177-227923630	PANC-1	pancreas:	n/a	n/a
29	MAX	chr1:227922341-227923346	ECC-1	luminal epithelium:	n/a	chr1:227922598-227922607
30	POLR2A	chr1:227922188-227923639	Hela-S3	cervix:	n/a	n/a
31	MYC	chr1:227922358-227923226	MCF10A-Er-Src	breast:	n/a	chr1:227922598-227922607
32	POLR2A	chr1:227922134-227923498	PFSK-1	brain:	n/a	n/a
33	POLR2A	chr1:227922088-227923604	GM12891	blood:	n/a	n/a
34	ZNF263	chr1:227922204-227924083	HEK293-T-REx	kidney:	n/a	chr1:227923299-227923308
35	POLR2A	chr1:227922147-227924196	K562	blood:	n/a	n/a
36	POLR2A	chr1:227922281-227923402	NB4	blood:	n/a	n/a
37	MAX	chr1:227922397-227923288	Hela-S3	cervix:	n/a	chr1:227922598-227922607
38	MYC	chr1:227922320-227923287	K562	blood:	n/a	chr1:227922598-227922607
39	POLR2A	chr1:227922080-227923603	SK-N-MC	brain:	n/a	n/a
40	MXI1	chr1:227922255-227923265	GM12878	blood:	n/a	n/a
41	ZNF143	chr1:227922326-227922523	K562	blood:	n/a	n/a
42	RCOR1	chr1:227922356-227922543	K562	blood:	n/a	n/a
43	SIN3A	chr1:227922290-227923338	H1-hESC	embryonic stem cell:	n/a	n/a
44	E2F6	chr1:227922405-227923259	H1-hESC	embryonic stem cell:	n/a	chr1:227922700-227922710
45	NR2F2	chr1:227922271-227923336	K562	blood:	n/a	n/a
46	MYC	chr1:227922340-227922495	MCF10A-Er-Src	breast:	n/a	n/a
47	CTCF	chr1:227922320-227922470	GM12875	blood:	n/a	n/a
48	POLR2A	chr1:227922297-227923498	MCF-7	breast:	n/a	n/a
49	CREB1	chr1:227922265-227923512	HepG2	liver:	n/a	n/a
50	SIN3AK20	chr1:227922234-227923408	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:227921116..227923050-chr1:228289460..228292114,2	MCF-7	breast:
2	chr1:227918805..227924684-chr1:227929963..227939883,12	K562	blood:
3	chr1:227750240..227752795-chr1:227921793..227923560,2	K562	blood:
4	chr1:227921956..227924183-chr1:227932541..227935696,3	MCF-7	breast:
5	chr1:227921488..227923041-chr1:228269667..228272192,2	MCF-7	breast:
6	chr1:227916221..227923035-chr1:228131852..228141791,18	MCF-7	breast:

Variant related genes	Relation type
SNAP47	TF binding region
JMJD4	TF binding region
ENSG00000181450	Chromatin interaction
ENSG00000143793	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000143816	Chromatin interaction
ENSG00000143740	Chromatin interaction
ENSG00000230005	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	esv3375515	chr1:227921854-227924702	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227921400-227922600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:227921600-227922600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
3	chr1:227921600-227922600	Flanking Active TSS	Brain Cingulate Gyrus	brain
4	chr1:227921600-227922600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:227921600-227922600	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr1:227921600-227922600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
7	chr1:227921600-227922600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr1:227921600-227923000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:227921600-227923000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:227921600-227923600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:227921600-227923600	Active TSS	Placenta Amnion	Placenta Amnion
12	chr1:227921600-227924200	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr1:227921600-227924200	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr1:227921800-227922600	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr1:227921800-227922600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:227921800-227922600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr1:227921800-227922600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:227921800-227922600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:227921800-227922600	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr1:227921800-227922600	Flanking Active TSS	Fetal Brain Female	brain
21	chr1:227921800-227922600	Flanking Active TSS	Fetal Muscle Trunk	muscle
22	chr1:227921800-227922600	Flanking Active TSS	Placenta	Placenta
23	chr1:227921800-227922600	Flanking Active TSS	Dnd41	blood
24	chr1:227921800-227922800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr1:227921800-227922800	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr1:227921800-227923800	Active TSS	GM12878-XiMat	blood
27	chr1:227921800-227924200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:227921800-227924200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:227921800-227924200	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr1:227921800-227924200	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr1:227921800-227924200	Active TSS	A549	lung
32	chr1:227922000-227922600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr1:227922000-227922600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr1:227922000-227922600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:227922000-227922600	Flanking Active TSS	Liver	Liver
36	chr1:227922000-227922600	Flanking Active TSS	Brain Angular Gyrus	brain
37	chr1:227922000-227922600	Flanking Active TSS	Fetal Lung	lung
38	chr1:227922000-227922600	Flanking Active TSS	Fetal Muscle Leg	muscle
39	chr1:227922000-227922600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr1:227922000-227922600	Flanking Active TSS	Right Ventricle	heart
41	chr1:227922000-227922600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr1:227922000-227922800	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr1:227922000-227922800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:227922000-227922800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr1:227922000-227923400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:227922000-227923600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr1:227922000-227923600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:227922000-227923600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:227922000-227923600	Active TSS	Psoas Muscle	Psoas
50	chr1:227922000-227923800	Active TSS	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links