Variant report

Variant	rs2869854
Chromosome Location	chr4:77099673-77099674
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	chr4:77058522..77060950-chr4:77099295..77101938,2	MCF-7	breast:
2	chr4:77067502..77069433-chr4:77097939..77100714,2	K562	blood:

Variant related genes	Relation type
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs12499900	1.00[CEU][hapmap]
rs12641190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13111705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13117802	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13119254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1441923	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1470191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1470194	0.98[EUR][1000 genomes]
rs1550556	0.96[EUR][1000 genomes]
rs17001416	1.00[CEU][hapmap]
rs17001588	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17001589	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17001604	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2034002	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2034003	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2053486	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2053487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2304813	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34022163	0.98[EUR][1000 genomes]
rs34334700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34974381	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35583533	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35783378	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36035650	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36081173	0.98[EUR][1000 genomes]
rs3796497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3853188	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3853189	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3853190	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3866353	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3866354	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4452450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4634246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859425	1.00[CEU][hapmap]
rs4859426	1.00[CEU][hapmap]
rs4859428	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859623	0.96[EUR][1000 genomes]
rs4859624	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859625	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859627	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859628	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859629	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4859631	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67653006	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67917805	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6824367	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6831345	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6851995	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72857046	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72857048	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7664889	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7691447	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs894244	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs894247	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894248	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594693	chr4:77033590-77101068	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv461558	chr4:77033725-77115553	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv594694	chr4:77033725-77115553	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1000539	chr4:77042356-77105492	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1000178	chr4:77053046-77113080	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv995458	chr4:77093764-77102178	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77070600-77113600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr4:77071200-77113600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:77078200-77100600	Weak transcription	K562	blood
4	chr4:77078600-77100800	Strong transcription	Placenta	Placenta
5	chr4:77079200-77100800	Strong transcription	Liver	Liver
6	chr4:77079400-77100000	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr4:77079400-77100800	Strong transcription	Fetal Intestine Large	intestine
8	chr4:77079400-77101400	Strong transcription	Fetal Muscle Trunk	muscle
9	chr4:77079400-77108200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr4:77079600-77101200	Strong transcription	Duodenum Mucosa	Duodenum
11	chr4:77079600-77101400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:77079800-77101000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr4:77080600-77113600	Weak transcription	Thymus	Thymus
14	chr4:77080800-77101200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:77080800-77101200	Strong transcription	NHDF-Ad	bronchial
16	chr4:77082400-77101400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:77082600-77100800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:77083200-77112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:77087000-77101400	Strong transcription	Fetal Lung	lung
20	chr4:77088200-77101400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:77090000-77113600	Weak transcription	A549	lung
22	chr4:77090200-77100600	Weak transcription	Stomach Mucosa	stomach
23	chr4:77090200-77113000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:77090200-77114800	Weak transcription	Hela-S3	cervix
25	chr4:77090400-77100800	Weak transcription	Fetal Heart	heart
26	chr4:77090400-77107000	Weak transcription	Aorta	Aorta
27	chr4:77091000-77100800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:77091000-77114200	Weak transcription	HMEC	breast
29	chr4:77092000-77100200	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr4:77092000-77101000	Strong transcription	Primary T cells from cord blood	blood
31	chr4:77092600-77101000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:77093400-77100800	Strong transcription	Primary B cells from cord blood	blood
33	chr4:77094400-77113800	Weak transcription	Fetal Thymus	thymus
34	chr4:77095000-77113400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr4:77095400-77101200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr4:77095400-77107000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:77095600-77099800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr4:77095600-77103600	Weak transcription	NHEK	skin
39	chr4:77095800-77107000	Weak transcription	Esophagus	oesophagus
40	chr4:77096000-77100600	Weak transcription	Colon Smooth Muscle	Colon
41	chr4:77096200-77107000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:77096200-77107000	Weak transcription	Spleen	Spleen
43	chr4:77096200-77113200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr4:77096200-77113400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:77096600-77100800	Weak transcription	Pancreas	Pancrea
46	chr4:77096600-77100800	Weak transcription	Right Ventricle	heart
47	chr4:77096600-77107000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:77096600-77107000	Weak transcription	Gastric	stomach
49	chr4:77096800-77100600	Weak transcription	Ovary	ovary
50	chr4:77096800-77114000	Weak transcription	Small Intestine	intestine

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