Variant report

Variant	rs12078868
Chromosome Location	chr1:226102168-226102169
allele	A/G
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	ZNF263	chr1:226102162-226102360	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:226069654..226072085-chr1:226101693..226103533,2	MCF-7	breast:
2	chr1:226038307..226042475-chr1:226101136..226103388,3	K562	blood:
3	chr1:226032713..226034460-chr1:226100032..226102843,2	MCF-7	breast:

Variant related genes	Relation type
LEFTY1	TF binding region
ENSG00000242861	Chromatin interaction
ENSG00000196187	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10915886	1.00[ASW][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.84[YRI][hapmap]
rs10915887	0.84[YRI][hapmap]
rs10915888	1.00[ASW][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.84[YRI][hapmap]
rs10915895	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10915902	0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs10915903	0.81[AMR][1000 genomes]
rs12071072	0.84[AFR][1000 genomes]
rs12071104	0.84[AFR][1000 genomes]
rs12074209	0.81[AFR][1000 genomes]
rs12074247	0.81[AFR][1000 genomes]
rs12080725	0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes]
rs12092868	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12094548	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35273824	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs35684337	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs56035614	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6700642	0.84[MKK][hapmap];0.81[AMR][1000 genomes]
rs74150558	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74150559	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74150561	0.92[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	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	esv3335650	chr1:226074720-226125458	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv3369235	chr1:226075748-226127738	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv468216	chr1:226078915-226135132	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv549267	chr1:226078915-226135132	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv535314	chr1:226087226-226128261	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking 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 miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226087000-226107200	Weak transcription	Psoas Muscle	Psoas
2	chr1:226087600-226103400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:226087600-226103600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:226087600-226104600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:226092200-226103200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:226096400-226103800	Weak transcription	Gastric	stomach
7	chr1:226097800-226102600	Weak transcription	Dnd41	blood
8	chr1:226097800-226103200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:226097800-226104600	Weak transcription	GM12878-XiMat	blood
10	chr1:226098200-226103000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:226098200-226103000	Weak transcription	NHEK	skin
12	chr1:226098200-226103200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:226098200-226103600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:226098400-226102800	Weak transcription	HMEC	breast
15	chr1:226098800-226103000	Weak transcription	Brain Anterior Caudate	brain
16	chr1:226098800-226105200	Weak transcription	K562	blood
17	chr1:226099000-226104800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:226099200-226102200	Weak transcription	Primary T cells from cord blood	blood
19	chr1:226099200-226102400	Weak transcription	Liver	Liver
20	chr1:226099200-226103000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:226099200-226103600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:226099200-226103800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:226099200-226103800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:226099200-226104200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:226099200-226104200	Weak transcription	NHLF	lung
26	chr1:226099200-226104400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:226099200-226105600	Weak transcription	Aorta	Aorta
28	chr1:226099200-226107200	Weak transcription	HUVEC	blood vessel
29	chr1:226099200-226107600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:226099200-226109000	Weak transcription	Colonic Mucosa	Colon
31	chr1:226099400-226102200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:226099400-226102200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:226099400-226102200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:226099400-226103200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:226099400-226103200	Weak transcription	Spleen	Spleen
36	chr1:226099400-226104600	Weak transcription	Fetal Kidney	kidney
37	chr1:226099400-226105200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:226099400-226106800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:226099400-226107200	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:226099400-226107400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:226099400-226109800	Weak transcription	Stomach Mucosa	stomach
42	chr1:226099600-226102400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:226099600-226102800	Weak transcription	Adipose Nuclei	Adipose
44	chr1:226099600-226103400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:226099600-226103400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr1:226099600-226103600	Weak transcription	Fetal Intestine Large	intestine
47	chr1:226099600-226104200	Weak transcription	Osteobl	bone
48	chr1:226099600-226104400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:226099600-226104400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:226099600-226104600	Weak transcription	Primary hematopoietic stem cells	blood

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