Variant report

Variant	rs540728336
Chromosome Location	chr1:227976467-227976468
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227973990..227976500-chr1:228134426..228136462,3	MCF-7	breast:
2	chr1:227967943..227969824-chr1:227975075..227977321,2	K562	blood:
3	chr1:227945394..227947244-chr1:227973849..227976801,2	MCF-7	breast:
4	chr1:227960240..227967392-chr1:227972741..227977657,8	K562	blood:
5	chr1:227921116..227924283-chr1:227974450..227977412,3	MCF-7	breast:
6	chr1:227974881..227977726-chr20:49346280..49347834,2	MCF-7	breast:
7	chr1:227973847..227976813-chr1:228134403..228136465,4	MCF-7	breast:
8	chr1:227974795..227976825-chr1:227979678..227981441,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNAP47-1	chr1:227975807-227979880	NONHSAT009949

No data

Variant related genes	Relation type
ENSG00000143740	Chromatin interaction
ENSG00000143816	Chromatin interaction
ENSG00000081692	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
8	nsv468238	chr1:227935762-228045748	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv549272	chr1:227935762-228045748	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
11	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
12	esv3441420	chr1:227974754-227977302	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv3380731	chr1:227975029-227977177	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227974600-227977000	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:227974800-227976800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:227974800-227977000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr1:227974800-227977200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr1:227974800-227977200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr1:227974800-227977400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:227975000-227976600	Active TSS	Aorta	Aorta
8	chr1:227975000-227976600	Active TSS	Fetal Kidney	kidney
9	chr1:227975000-227977200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr1:227975200-227976600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:227975200-227976600	Active TSS	H9 Cell Line	embryonic stem cell
12	chr1:227975200-227976600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:227975200-227976600	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr1:227975200-227976600	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr1:227975200-227976600	Active TSS	Psoas Muscle	Psoas
16	chr1:227975200-227976800	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr1:227975200-227976800	Active TSS	A549	lung
18	chr1:227975200-227976800	Active TSS	NHDF-Ad	bronchial
19	chr1:227975200-227977000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:227975200-227977000	Active TSS	Rectal Smooth Muscle	rectum
21	chr1:227975200-227977200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr1:227975200-227977600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr1:227975400-227976600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
24	chr1:227975400-227976600	Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr1:227975400-227976600	Active TSS	Esophagus	oesophagus
26	chr1:227975400-227976800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:227975400-227976800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:227975400-227976800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:227975600-227976600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:227975600-227976600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr1:227975600-227976600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr1:227975600-227976600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr1:227975600-227976600	Active TSS	GM12878-XiMat	blood
34	chr1:227975600-227976600	Active TSS	Hela-S3	cervix
35	chr1:227975600-227976600	Bivalent/Poised TSS	HepG2	liver
36	chr1:227975600-227976600	Active TSS	HSMMtube	muscle
37	chr1:227975600-227976600	Active TSS	NHLF	lung
38	chr1:227975600-227976800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:227975600-227976800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
40	chr1:227975600-227976800	Active TSS	Rectal Mucosa Donor 31	rectum
41	chr1:227975600-227977000	Active TSS	Primary hematopoietic stem cells	blood
42	chr1:227975800-227976600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:227975800-227977000	Active TSS	HSMM	muscle
44	chr1:227976000-227976800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
45	chr1:227976000-227976800	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:227976000-227976800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
47	chr1:227976000-227976800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
48	chr1:227976000-227977000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
49	chr1:227976200-227976600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:227976200-227976600	Flanking Active TSS	Duodenum Mucosa	Duodenum

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