Variant report

Variant	rs3008633
Chromosome Location	chr1:222844840-222844841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222844464..222847879-chr1:222884491..222887839,3	K562	blood:
2	chr1:222843901..222845494-chr1:222846340..222847859,2	K562	blood:

Variant related genes	Relation type
ENSG00000162819	Chromatin interaction
ENSG00000186063	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1053316	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17163384	0.82[MEX][hapmap]
rs17163431	0.82[MEX][hapmap]
rs2291833	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2936025	0.95[CHD][hapmap];0.85[JPT][hapmap]
rs3008611	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs3008613	0.85[JPT][hapmap]
rs3008620	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3008634	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008635	0.95[CHD][hapmap];0.85[JPT][hapmap]
rs3008639	0.95[CHD][hapmap];0.85[JPT][hapmap]
rs34290674	0.95[CHD][hapmap];0.85[JPT][hapmap]
rs35684750	0.83[ASW][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs35762933	0.83[ASW][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs73124884	0.85[ASN][1000 genomes]
rs73124898	0.83[ASN][1000 genomes]
rs7520650	0.80[AFR][1000 genomes];0.81[ASN][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	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222827000-222845400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:222835200-222884600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:222836600-222849600	Weak transcription	Stomach Mucosa	stomach
4	chr1:222839000-222845400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:222839000-222849000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:222839000-222849000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:222839000-222854400	Weak transcription	Lung	lung
8	chr1:222839000-222859800	Weak transcription	Small Intestine	intestine
9	chr1:222839000-222877400	Weak transcription	Psoas Muscle	Psoas
10	chr1:222839000-222884600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:222839200-222861200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:222839400-222845400	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:222839600-222884600	Weak transcription	Esophagus	oesophagus
14	chr1:222839800-222847200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:222839800-222848800	Weak transcription	Right Ventricle	heart
16	chr1:222839800-222859600	Weak transcription	Brain Angular Gyrus	brain
17	chr1:222839800-222859600	Weak transcription	Fetal Brain Male	brain
18	chr1:222840000-222845800	Weak transcription	Brain Substantia Nigra	brain
19	chr1:222840000-222884600	Weak transcription	Colonic Mucosa	Colon
20	chr1:222841000-222859600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:222841200-222845000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:222841200-222845200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:222841200-222866200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:222841200-222883400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:222841400-222847400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:222841400-222847400	Weak transcription	HUVEC	blood vessel
27	chr1:222841400-222847400	Weak transcription	K562	blood
28	chr1:222841400-222848800	Weak transcription	Brain Anterior Caudate	brain
29	chr1:222841400-222883200	Weak transcription	Fetal Heart	heart
30	chr1:222842600-222850000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:222842600-222850000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr1:222842800-222846400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:222842800-222846400	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr1:222842800-222849600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:222842800-222849800	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:222842800-222867800	Strong transcription	Primary B cells from peripheral blood	blood
37	chr1:222843200-222845200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
38	chr1:222843200-222849200	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:222843200-222849200	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr1:222843200-222849400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:222843200-222849400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:222843200-222849600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:222843200-222849800	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr1:222843200-222849800	Strong transcription	Osteobl	bone
45	chr1:222843200-222850200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:222843200-222850600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:222843200-222850800	Strong transcription	NH-A	brain
48	chr1:222843400-222845000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr1:222843400-222845400	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr1:222843400-222846000	Strong transcription	A549	lung

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