Variant report

Variant	rs11802856
Chromosome Location	chr1:46809016-46809017
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	chr1:46808184-46809855	K562	blood:	n/a	n/a
2	POLR2A	chr1:46805002-46809990	K562	blood:	n/a	n/a
3	EBF1	chr1:46807424-46809213	GM12878	blood:	n/a	n/a
4	HEY1	chr1:46808354-46809141	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:46763061..46775715-chr1:46803221..46815018,50	K562	blood:
2	chr1:46763061..46775205-chr1:46803159..46817121,53	K562	blood:
3	chr1:46775398..46777226-chr1:46806955..46809185,2	K562	blood:

Variant related genes	Relation type
NSUN4	TF binding region
ENSG00000173660	Chromatin interaction
ENSG00000132128	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11211267	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11804220	1.00[EUR][1000 genomes]
rs11804982	1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12086460	1.00[EUR][1000 genomes]
rs12096333	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35563048	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3737742	1.00[TSI][hapmap]
rs3931457	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57638901	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6688130	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6703596	1.00[EUR][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	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic 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 target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv470711	chr1:46660295-46810530	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv12311	chr1:46805652-46810297	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv546162	chr1:46807597-46870761	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv546163	chr1:46808042-46809782	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv546164	chr1:46808426-46809782	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46807000-46810000	Enhancers	Fetal Heart	heart
2	chr1:46807000-46827200	Weak transcription	Fetal Brain Male	brain
3	chr1:46807200-46809400	Enhancers	Left Ventricle	heart
4	chr1:46807200-46809400	Weak transcription	Thymus	Thymus
5	chr1:46807200-46810200	Weak transcription	Aorta	Aorta
6	chr1:46807200-46810600	Weak transcription	Fetal Kidney	kidney
7	chr1:46807200-46818400	Weak transcription	Small Intestine	intestine
8	chr1:46807200-46827600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:46807400-46809200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:46807400-46809400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:46807400-46809400	Genic enhancers	Fetal Muscle Trunk	muscle
12	chr1:46807400-46809400	Genic enhancers	Fetal Muscle Leg	muscle
13	chr1:46807400-46809400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:46807400-46810200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:46807400-46810200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:46807400-46810600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:46807400-46813200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:46807400-46815200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:46807400-46820400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:46807400-46831800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:46807400-46832200	Strong transcription	Fetal Stomach	stomach
22	chr1:46807600-46809200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:46807600-46809400	Weak transcription	Fetal Brain Female	brain
24	chr1:46807600-46809600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:46807600-46809600	Weak transcription	Brain Germinal Matrix	brain
26	chr1:46807600-46809600	Weak transcription	Brain Substantia Nigra	brain
27	chr1:46807600-46809600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:46807600-46810200	Weak transcription	Fetal Lung	lung
29	chr1:46807600-46810400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:46807600-46810400	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:46807600-46810800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:46807600-46810800	Weak transcription	A549	lung
33	chr1:46807600-46813000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:46807600-46815200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:46807600-46815200	Weak transcription	Psoas Muscle	Psoas
36	chr1:46807600-46835400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:46807600-46844600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:46807800-46809200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:46807800-46809200	Weak transcription	HSMMtube	muscle
40	chr1:46807800-46809400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:46807800-46809400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:46807800-46809400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
43	chr1:46807800-46809600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:46807800-46809800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:46807800-46809800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr1:46807800-46809800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr1:46807800-46809800	Weak transcription	Esophagus	oesophagus
48	chr1:46807800-46810000	Weak transcription	Colonic Mucosa	Colon
49	chr1:46807800-46810200	Weak transcription	Brain Angular Gyrus	brain
50	chr1:46807800-46810200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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