Variant report

Variant	rs10494749
Chromosome Location	chr1:197168233-197168234
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	POLR2A	chr1:197167458-197168530	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr1:197168070-197168410	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr1:197167830-197168438	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr1:197168153-197168394	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:197152680..197155309-chr1:197165847..197169413,3	MCF-7	breast:
2	chr1:197167660..197168424-chr7:117707343..117708112,2	MCF-7	breast:
3	chr1:197153884..197156331-chr1:197167263..197169035,2	K562	blood:

Variant related genes	Relation type
CRB1	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1034162	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10429911	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10494748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10494750	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10494751	0.84[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10732295	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10732296	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10801594	1.00[CHB][hapmap]
rs11800461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11801772	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11803081	1.00[AMR][1000 genomes]
rs11808524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11808883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11809963	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11810041	0.85[AMR][1000 genomes]
rs11811295	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11811814	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1337165	1.00[AMR][1000 genomes]
rs1412631	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1415217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1556763	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1571964	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16841212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841214	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841219	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841220	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841237	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841270	1.00[AMR][1000 genomes]
rs1759013	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1794003	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4915378	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs59820773	1.00[ASN][1000 genomes]
rs61170532	1.00[AMR][1000 genomes]
rs61172533	1.00[ASN][1000 genomes]
rs6677082	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6700604	1.00[ASN][1000 genomes]
rs6702338	1.00[ASN][1000 genomes]
rs6702739	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6703400	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7520503	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7534439	1.00[JPT][hapmap]
rs7535048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[ASN][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	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	26 gene(s)	inside rSNPs	diseases
2	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv2757767	chr1:196977799-197169772	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv873071	chr1:197079671-197187605	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv873072	chr1:197079671-197221248	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv548871	chr1:197106604-197168233	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic 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	6 gene(s)	inside rSNPs	diseases
8	nsv873073	chr1:197107074-197221248	Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	esv2445525	chr1:197167182-197168584	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197116600-197169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:197125400-197168400	Weak transcription	Psoas Muscle	Psoas
3	chr1:197125600-197169600	Weak transcription	Esophagus	oesophagus
4	chr1:197126400-197169600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:197152400-197168600	Weak transcription	Stomach Mucosa	stomach
6	chr1:197157400-197168400	Weak transcription	Left Ventricle	heart
7	chr1:197157400-197169400	Weak transcription	Colonic Mucosa	Colon
8	chr1:197157400-197169600	Weak transcription	Pancreas	Pancrea
9	chr1:197159400-197169600	Weak transcription	Gastric	stomach
10	chr1:197159400-197169800	Weak transcription	Lung	lung
11	chr1:197159600-197168600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:197159600-197169200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:197159600-197169800	Weak transcription	Spleen	Spleen
14	chr1:197159800-197168600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:197159800-197169600	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr1:197160600-197169200	Weak transcription	Fetal Stomach	stomach
17	chr1:197161000-197169200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:197161000-197169400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:197161000-197169400	Weak transcription	Placenta	Placenta
20	chr1:197161200-197168600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:197161600-197168800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:197163400-197169400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:197163600-197168800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:197164000-197168600	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr1:197164000-197168800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr1:197164000-197169200	Active TSS	GM12878-XiMat	blood
27	chr1:197164600-197168400	Enhancers	Hela-S3	cervix
28	chr1:197164800-197169400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr1:197165000-197169400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:197165600-197169200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:197166200-197170000	Flanking Active TSS	Dnd41	blood
32	chr1:197166400-197168400	Active TSS	Brain Anterior Caudate	brain
33	chr1:197166400-197168600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:197166400-197171400	Active TSS	K562	blood
35	chr1:197166400-197171600	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr1:197166400-197171600	Active TSS	Right Atrium	heart
37	chr1:197166600-197171600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:197166800-197168400	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr1:197166800-197168600	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr1:197166800-197168600	Active TSS	NHLF	lung
41	chr1:197166800-197168800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:197166800-197169200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:197166800-197169800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:197166800-197171400	Active TSS	HSMMtube	muscle
45	chr1:197166800-197171600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:197166800-197171800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:197167000-197168600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:197167000-197168800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr1:197167000-197169600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:197167200-197168400	Weak transcription	Primary monocytes fromperipheralblood	blood

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