Variant report

Variant	rs12035875
Chromosome Location	chr1:228672965-228672966
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	ARID3A	chr1:228672918-228673477	K562	blood:	n/a	chr1:228673191-228673207
2	ZMIZ1	chr1:228672932-228673105	K562	blood:	n/a	n/a
3	FOS	chr1:228672757-228673115	HUVEC	blood vessel:	n/a	chr1:228672876-228672887
4	FOS	chr1:228672750-228673202	MCF10A-Er-Src	breast:	n/a	chr1:228672876-228672887
5	FOXA1	chr1:228672643-228673150	HepG2	liver:	n/a	n/a
6	FOXA1	chr1:228672791-228673170	HepG2	liver:	n/a	n/a
7	FOS	chr1:228672753-228673105	MCF10A-Er-Src	breast:	n/a	chr1:228672876-228672887
8	POLR2A	chr1:228672781-228673091	HCT-116	colon:	n/a	n/a
9	FOXA2	chr1:228672785-228673079	HepG2	liver:	n/a	n/a
10	NR2F2	chr1:228672721-228673020	K562	blood:	n/a	n/a
11	POLR2A	chr1:228672940-228673401	K562	blood:	n/a	n/a
12	FOS	chr1:228672750-228673144	MCF10A-Er-Src	breast:	n/a	chr1:228672876-228672887
13	JUND	chr1:228672818-228672983	HepG2	liver:	n/a	n/a
14	FOXA2	chr1:228672611-228673065	A549	lung:	n/a	n/a
15	FOS	chr1:228672788-228672988	MCF10A-Er-Src	breast:	n/a	chr1:228672876-228672887
16	TBL1XR1	chr1:228672905-228673105	K562	blood:	n/a	n/a
17	FOXA2	chr1:228672701-228673209	A549	lung:	n/a	n/a
18	CBX3	chr1:228672786-228673159	K562	blood:	n/a	n/a
19	FOXA1	chr1:228672774-228673042	HepG2	liver:	n/a	n/a
20	JUND	chr1:228672782-228672989	HepG2	liver:	n/a	n/a
21	FOSL2	chr1:228672693-228673190	A549	lung:	n/a	n/a
22	CEBPB	chr1:228672830-228673151	IMR90	lung:	n/a	n/a
23	TBP	chr1:228672906-228672999	K562	blood:	n/a	n/a
24	FOSL1	chr1:228672699-228673038	K562	blood:	n/a	n/a
25	FOSL2	chr1:228672696-228673008	HepG2	liver:	n/a	n/a
26	ZNF384	chr1:228672791-228673345	K562	blood:	n/a	n/a
27	RCOR1	chr1:228672788-228672983	K562	blood:	n/a	n/a
28	STAT3	chr1:228672929-228672967	MCF10A-Er-Src	breast:	n/a	chr1:228672943-228672954
29	EP300	chr1:228672908-228673456	K562	blood:	n/a	chr1:228673001-228673015
30	JUND	chr1:228672744-228673439	K562	blood:	n/a	n/a
31	MYC	chr1:228672817-228673110	MCF10A-Er-Src	breast:	n/a	n/a
32	FOXA1	chr1:228672782-228673111	HepG2	liver:	n/a	n/a
33	NR2F2	chr1:228672481-228673428	K562	blood:	n/a	n/a
34	JUN	chr1:228672601-228678958	K562	blood:	n/a	chr1:228677697-228677705 chr1:228678292-228678303

No.	Distal block	Cell Line	Cell type
1	chr1:228665457..228668027-chr1:228670645..228673009,2	MCF-7	breast:
2	chr1:228642342..228647806-chr1:228672380..228678428,13	MCF-7	breast:
3	chr1:228671614..228676496-chr1:228676543..228681096,6	MCF-7	breast:
4	chr1:228643230..228649256-chr1:228671672..228678578,15	MCF-7	breast:

Variant related genes	Relation type
RNF187	TF binding region
ENSG00000181218	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000168159	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12034519	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
5	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
9	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
11	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
12	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228667400-228673600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:228667400-228674000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:228667600-228673600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr1:228667600-228673800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:228667600-228674000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr1:228667800-228673800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr1:228667800-228674000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:228668000-228673200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:228668000-228673600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr1:228668000-228673600	Weak transcription	Pancreas	Pancrea
11	chr1:228668000-228674000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:228668200-228673200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:228668200-228673800	Weak transcription	Fetal Intestine Small	intestine
14	chr1:228669000-228673000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:228670800-228673800	Weak transcription	GM12878-XiMat	blood
16	chr1:228672000-228673800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:228672200-228673800	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr1:228672600-228673800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:228672800-228673000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:228672800-228673000	Enhancers	K562	blood
21	chr1:228672800-228673200	Enhancers	HepG2	liver
22	chr1:228672800-228673400	Enhancers	Stomach Mucosa	stomach
23	chr1:228672800-228673800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr1:228672800-228673800	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr1:228672800-228674000	Enhancers	HUVEC	blood vessel

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