Variant report

Variant	rs34560898
Chromosome Location	chr1:227923067-227923068
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:548)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:548 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr1:227922920-227923183	K562	blood:	n/a	n/a
2	ZBTB33	chr1:227922751-227923211	A549	lung:	n/a	n/a
3	EP300	chr1:227922787-227923298	T-47D	breast:	n/a	n/a
4	POLR2A	chr1:227922714-227923494	H1-neurons	neurons:	n/a	n/a
5	SIX5	chr1:227922849-227923209	GM12878	blood:	n/a	n/a
6	STAT3	chr1:227922910-227923181	MCF10A-Er-Src	breast:	n/a	n/a
7	HEY1	chr1:227922641-227923404	HepG2	liver:	n/a	n/a
8	CTCF	chr1:227922979-227923073	NHEK	skin:	n/a	n/a
9	MAX	chr1:227922506-227923248	HepG2	liver:	n/a	chr1:227922598-227922607
10	GABPA	chr1:227922755-227923279	HL-60	blood:	n/a	n/a
11	RFX5	chr1:227922947-227923190	K562	blood:	n/a	n/a
12	POLR2A	chr1:227922095-227923743	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr1:227922324-227923419	K562	blood:	n/a	n/a
14	CHD2	chr1:227922770-227923296	HepG2	liver:	n/a	n/a
15	CREB1	chr1:227922679-227923311	A549	lung:	n/a	n/a
16	MYC	chr1:227922828-227923215	HUVEC	blood vessel:	n/a	n/a
17	TCF12	chr1:227922345-227923575	A549	lung:	n/a	chr1:227922625-227922635
18	IRF4	chr1:227922804-227923303	GM12878	blood:	n/a	n/a
19	TBL1XR1	chr1:227922862-227923224	K562	blood:	n/a	n/a
20	POLR2A	chr1:227922680-227923445	GM12891	blood:	n/a	n/a
21	SIX5	chr1:227922871-227923250	K562	blood:	n/a	n/a
22	TAF1	chr1:227922835-227923225	GM12891	blood:	n/a	n/a
23	MAX	chr1:227922265-227923415	MCF-7	breast:	n/a	chr1:227922598-227922607
24	POLR2A	chr1:227922721-227923332	GM12892	blood:	n/a	n/a
25	FOSL2	chr1:227922872-227923132	A549	lung:	n/a	n/a
26	POLR2A	chr1:227922684-227923338	HUVEC	blood vessel:	n/a	n/a
27	BRCA1	chr1:227922876-227923207	Hela-S3	cervix:	n/a	n/a
28	BHLHE40	chr1:227922815-227923247	HepG2	liver:	n/a	n/a
29	SIN3AK20	chr1:227922823-227923257	H1-hESC	embryonic stem cell:	n/a	n/a
30	TAF1	chr1:227922716-227923432	H1-neurons	neurons:	n/a	n/a
31	ATF3	chr1:227922794-227923294	A549	lung:	n/a	n/a
32	POLR2A	chr1:227922205-227924256	PBDE	blood:	n/a	n/a
33	YY1	chr1:227922703-227923320	GM12878	blood:	n/a	n/a
34	SIN3AK20	chr1:227922266-227923575	K562	blood:	n/a	n/a
35	REST	chr1:227922861-227923178	SK-N-SH	brain:	n/a	n/a
36	SIN3AK20	chr1:227922540-227923490	PANC-1	pancreas:	n/a	n/a
37	BRCA1	chr1:227922831-227923202	H1-hESC	embryonic stem cell:	n/a	n/a
38	ELK1	chr1:227922528-227923283	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr1:227922479-227923559	A549	lung:	n/a	n/a
40	GABPA	chr1:227922771-227923249	HepG2	liver:	n/a	n/a
41	GATA3	chr1:227922673-227923358	A549	lung:	n/a	chr1:227923238-227923246
42	GABPA	chr1:227922604-227923323	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr1:227922726-227923421	HepG2	liver:	n/a	n/a
44	SRF	chr1:227922910-227923116	K562	blood:	n/a	n/a
45	CEBPD	chr1:227922725-227923408	HepG2	liver:	n/a	n/a
46	MYC	chr1:227922282-227923383	NB4	blood:	n/a	chr1:227922598-227922607
47	CREB1	chr1:227922690-227923346	GM12878	blood:	n/a	n/a
48	TCF12	chr1:227922612-227923347	ECC-1	luminal epithelium:	n/a	chr1:227922625-227922635
49	MAZ	chr1:227922175-227924196	IMR90	lung:	n/a	chr1:227922598-227922607
50	ZBTB33	chr1:227922783-227923141	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227922958..227924817-chr1:228133058..228135872,2	MCF-7	breast:
2	chr1:227918805..227924684-chr1:227929963..227939883,12	K562	blood:
3	chr1:227750240..227752795-chr1:227921793..227923560,2	K562	blood:
4	chr1:227923000..227925656-chr1:228268639..228271303,2	MCF-7	breast:
5	chr1:227922748..227923393-chr18:10525883..10526533,2	Hela-S3	cervix:
6	chr1:227921956..227924183-chr1:227932541..227935696,3	MCF-7	breast:
7	chr1:227922541..227923238-chr20:21283483..21284425,2	HCT-116	colon:

No data

Variant related genes	Relation type
JMJD4	TF binding region
SNAP47	TF binding region
ENSG00000134265	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000088930	Chromatin interaction
ENSG00000230005	Chromatin interaction
ENSG00000143816	Chromatin interaction
ENSG00000181450	Chromatin interaction
ENSG00000143740	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs13373816	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	chr1:227921600-227923600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:227921600-227923600	Active TSS	Placenta Amnion	Placenta Amnion
3	chr1:227921600-227924200	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr1:227921600-227924200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:227921800-227923800	Active TSS	GM12878-XiMat	blood
6	chr1:227921800-227924200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:227921800-227924200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:227921800-227924200	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:227921800-227924200	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr1:227921800-227924200	Active TSS	A549	lung
11	chr1:227922000-227923400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:227922000-227923600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr1:227922000-227923600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:227922000-227923600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:227922000-227923600	Active TSS	Psoas Muscle	Psoas
16	chr1:227922000-227923800	Active TSS	H1 Cell Line	embryonic stem cell
17	chr1:227922000-227923800	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr1:227922000-227923800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:227922000-227923800	Active TSS	Ovary	ovary
20	chr1:227922000-227923800	Active TSS	Hela-S3	cervix
21	chr1:227922000-227923800	Active TSS	K562	blood
22	chr1:227922000-227924000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:227922000-227924000	Active TSS	H9 Cell Line	embryonic stem cell
24	chr1:227922000-227924000	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr1:227922000-227924000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:227922000-227924000	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr1:227922000-227924000	Active TSS	Fetal Kidney	kidney
28	chr1:227922000-227924000	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr1:227922000-227924200	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr1:227922000-227924200	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr1:227922200-227923600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:227922200-227923600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:227922200-227923600	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr1:227922200-227923600	Active TSS	Osteobl	bone
35	chr1:227922200-227923800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:227922200-227923800	Active TSS	Aorta	Aorta
37	chr1:227922200-227923800	Active TSS	HSMMtube	muscle
38	chr1:227922200-227923800	Active TSS	NHEK	skin
39	chr1:227922200-227923800	Active TSS	NHLF	lung
40	chr1:227922200-227924000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:227922200-227924000	Active TSS	Muscle Satellite Cultured Cells	--
42	chr1:227922200-227924000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:227922200-227924200	Active TSS	Fetal Intestine Large	intestine
44	chr1:227922400-227923400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:227922400-227923400	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr1:227922400-227923400	Active TSS	Esophagus	oesophagus
47	chr1:227922400-227923400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr1:227922400-227923400	Active TSS	Fetal Brain Male	brain
49	chr1:227922400-227923600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:227922400-227923600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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