Variant report

Variant	rs16841808
Chromosome Location	chr1:241683942-241683943
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	IRF1	chr1:241682771-241684009	K562	blood:	n/a	chr1:241683832-241683842 chr1:241683595-241683609 chr1:241683060-241683074 chr1:241683592-241683605 chr1:241683928-241683937 chr1:241683927-241683936
2	MXI1	chr1:241681747-241684092	SK-N-SH	brain:	n/a	n/a
3	HCFC1	chr1:241682603-241684410	Hela-S3	cervix:	n/a	n/a
4	BRCA1	chr1:241682758-241684056	Hela-S3	cervix:	n/a	n/a
5	TBL1XR1	chr1:241682889-241684119	K562	blood:	n/a	n/a
6	TBP	chr1:241682846-241684360	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr1:241683278-241684065	K562	blood:	n/a	n/a
8	ARID3A	chr1:241683097-241684070	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:241683433..241685881-chr1:241689141..241691385,3	MCF-7	breast:
2	chr1:241681898..241684060-chr1:242010602..242013002,4	K562	blood:
3	chr1:241680902..241684541-chr1:242009942..242012706,4	K562	blood:

Variant related genes	Relation type
FH	TF binding region
ENSG00000174371	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10802969	0.87[EUR][1000 genomes]
rs10926505	0.87[EUR][1000 genomes]
rs10926508	0.87[EUR][1000 genomes]
rs10926510	0.87[EUR][1000 genomes]
rs12064150	0.87[EUR][1000 genomes]
rs12076255	0.87[EUR][1000 genomes]
rs12079341	0.87[EUR][1000 genomes]
rs2275162	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3765802	0.87[EUR][1000 genomes]
rs3765803	0.88[ASN][1000 genomes]
rs3765804	0.87[EUR][1000 genomes]
rs3819976	0.87[EUR][1000 genomes]
rs4659609	0.87[EUR][1000 genomes]
rs4660101	0.87[EUR][1000 genomes]
rs56957678	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58766151	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59625977	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60043538	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60673334	0.84[ASN][1000 genomes]
rs61543265	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61737760	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6429277	0.87[EUR][1000 genomes]
rs6429278	0.87[EUR][1000 genomes]
rs66482665	0.87[EUR][1000 genomes]
rs66497254	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66626588	0.88[ASN][1000 genomes]
rs66669018	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66710178	0.87[EUR][1000 genomes]
rs6678986	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679186	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66799800	0.96[ASN][1000 genomes]
rs6681649	0.87[EUR][1000 genomes]
rs6684064	0.87[EUR][1000 genomes]
rs6687609	0.87[EUR][1000 genomes]
rs6690411	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698519	0.87[EUR][1000 genomes]
rs67219057	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67267325	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67439618	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67528386	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67794990	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67802946	0.82[EUR][1000 genomes]
rs68119865	0.84[ASN][1000 genomes]
rs68147305	0.87[EUR][1000 genomes]
rs72766004	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135296	0.88[ASN][1000 genomes]
rs73137530	0.87[EUR][1000 genomes]
rs7539730	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv949442	chr1:241432051-241730054	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv873371	chr1:241667244-241747838	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv3394983	chr1:241681554-241684102	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241680600-241684000	Active TSS	A549	lung
2	chr1:241680800-241684000	Active TSS	HMEC	breast
3	chr1:241681200-241684000	Active TSS	NHDF-Ad	bronchial
4	chr1:241681400-241684000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:241681600-241684000	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr1:241681600-241684000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:241681800-241684000	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr1:241681800-241684000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:241682000-241684200	Active TSS	Duodenum Mucosa	Duodenum
10	chr1:241682000-241684200	Active TSS	K562	blood
11	chr1:241682200-241684000	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr1:241682200-241684000	Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr1:241682200-241684000	Active TSS	Fetal Brain Female	brain
14	chr1:241682400-241684000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:241682400-241684000	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr1:241682400-241684000	Active TSS	Thymus	Thymus
17	chr1:241682400-241684200	Active TSS	HepG2	liver
18	chr1:241682800-241684000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:241683000-241684000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:241683200-241684000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:241683200-241684000	Active TSS	Right Atrium	heart
22	chr1:241683400-241684000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:241683400-241684200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:241683600-241684000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:241683600-241684000	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr1:241683600-241684000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:241683600-241684000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr1:241683600-241684200	Flanking Active TSS	Dnd41	blood
29	chr1:241683800-241684000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:241683800-241684000	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr1:241683800-241684000	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr1:241683800-241684000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr1:241683800-241684000	Active TSS	Liver	Liver
34	chr1:241683800-241684000	Enhancers	Brain Cingulate Gyrus	brain
35	chr1:241683800-241684000	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr1:241683800-241684000	Enhancers	GM12878-XiMat	blood
37	chr1:241683800-241684000	Flanking Active TSS	Hela-S3	cervix
38	chr1:241683800-241684000	Bivalent Enhancer	HUVEC	blood vessel
39	chr1:241683800-241684200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:241683800-241684200	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr1:241683800-241684200	Enhancers	Brain Germinal Matrix	brain
42	chr1:241683800-241684200	Flanking Active TSS	NHEK	skin

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