Variant report

Variant	rs6427694
Chromosome Location	chr1:154465065-154465066
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	NFIC	chr1:154464494-154465122	GM12878	blood:	n/a	n/a
2	CUX1	chr1:154464614-154465267	GM12878	blood:	n/a	n/a
3	RUNX3	chr1:154464264-154465102	GM12878	blood:	n/a	n/a
4	ZEB1	chr1:154464672-154465102	GM12878	blood:	n/a	n/a
5	RUNX3	chr1:154464292-154465185	GM12878	blood:	n/a	n/a
6	EBF1	chr1:154464474-154465450	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
SHE	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1113142	1.00[EUR][1000 genomes]
rs11265605	1.00[EUR][1000 genomes]
rs11265630	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1194591	1.00[EUR][1000 genomes]
rs1194594	1.00[EUR][1000 genomes]
rs1194597	1.00[EUR][1000 genomes]
rs1194601	1.00[EUR][1000 genomes]
rs1205590	1.00[EUR][1000 genomes]
rs1685625	1.00[EUR][1000 genomes]
rs1685626	1.00[EUR][1000 genomes]
rs1817688	1.00[EUR][1000 genomes]
rs2340487	1.00[EUR][1000 genomes]
rs4078519	1.00[EUR][1000 genomes]
rs4240873	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4393148	0.94[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4474240	0.83[ASW][hapmap]
rs4520411	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845369	1.00[EUR][1000 genomes]
rs4845632	0.89[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845646	0.88[ASW][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55649582	1.00[EUR][1000 genomes]
rs55857358	1.00[EUR][1000 genomes]
rs6666943	1.00[EUR][1000 genomes]
rs6678164	0.82[ASW][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6681961	0.84[AFR][1000 genomes]
rs6683078	0.89[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6684225	0.82[ASW][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6685108	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs715737	1.00[EUR][1000 genomes]
rs7515974	0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7527520	1.00[EUR][1000 genomes]
rs7529744	1.00[MEX][hapmap]
rs7530737	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7537595	1.00[EUR][1000 genomes]
rs7556118	1.00[EUR][1000 genomes]
rs9659545	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9728545	0.81[AFR][1000 genomes]
rs9804125	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	esv1815481	chr1:154465065-154475033	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154441600-154465200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:154451600-154465600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:154458600-154469000	Weak transcription	Small Intestine	intestine
4	chr1:154459400-154465600	Weak transcription	Liver	Liver
5	chr1:154461400-154466400	Enhancers	Spleen	Spleen
6	chr1:154461800-154465600	Enhancers	Adipose Nuclei	Adipose
7	chr1:154461800-154465800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:154461800-154467000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:154461800-154473800	Weak transcription	Pancreas	Pancrea
10	chr1:154462800-154465400	Enhancers	Primary B cells from cord blood	blood
11	chr1:154462800-154467200	Enhancers	Primary B cells from peripheral blood	blood
12	chr1:154463000-154468000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:154463200-154466200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:154463200-154467600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:154463600-154465400	Genic enhancers	HUVEC	blood vessel
16	chr1:154463800-154465400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:154464000-154466600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr1:154464000-154472400	Weak transcription	Lung	lung
19	chr1:154464200-154465400	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr1:154464200-154465400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:154464200-154465400	Enhancers	Placenta	Placenta
22	chr1:154464200-154465800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:154464200-154466600	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr1:154464200-154466800	Enhancers	Primary hematopoietic stem cells	blood
25	chr1:154464200-154467600	Weak transcription	Right Ventricle	heart
26	chr1:154464400-154465600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:154464600-154465800	Enhancers	Primary T cells from cord blood	blood
28	chr1:154464600-154465800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:154464600-154466000	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:154464600-154466000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:154464600-154466400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:154464600-154466600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr1:154464600-154466600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr1:154464600-154467000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:154464800-154465400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:154464800-154466000	Bivalent Enhancer	Fetal Thymus	thymus
37	chr1:154464800-154466200	Enhancers	Brain Anterior Caudate	brain
38	chr1:154464800-154466600	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr1:154464800-154466600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr1:154464800-154466600	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr1:154464800-154466600	Enhancers	GM12878-XiMat	blood
42	chr1:154464800-154466800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:154464800-154467400	Enhancers	Primary T cells fromperipheralblood	blood
44	chr1:154464800-154469800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:154465000-154465200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:154465000-154465200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr1:154465000-154465400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:154465000-154466600	Enhancers	K562	blood
49	chr1:154465000-154466600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr1:154465000-154467000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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