Variant report

Variant	rs10890410
Chromosome Location	chr1:47161264-47161265
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47160988..47163658-chr1:47182412..47184770,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159658	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10890414	0.97[ASN][1000 genomes]
rs11211343	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11211347	0.86[ASN][1000 genomes]
rs11801744	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[ASN][1000 genomes]
rs12060032	0.83[ASN][1000 genomes]
rs12562113	0.88[ASN][1000 genomes]
rs12566278	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12568734	0.97[ASN][1000 genomes]
rs1258055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1258058	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[ASN][1000 genomes]
rs1258063	0.86[ASN][1000 genomes]
rs1258064	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1258065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1258066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1258068	0.88[ASN][1000 genomes]
rs1258072	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs1268714	0.88[ASN][1000 genomes]
rs1273237	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.88[ASN][1000 genomes]
rs13374909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1745376	0.88[ASN][1000 genomes]
rs1933932	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]
rs2146560	0.88[ASN][1000 genomes]
rs2181412	0.88[ASN][1000 genomes]
rs2241863	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2241864	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2439442	0.96[ASN][1000 genomes]
rs2476153	0.88[ASN][1000 genomes]
rs2476155	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2476156	0.88[ASN][1000 genomes]
rs2476157	0.94[ASN][1000 genomes]
rs2476159	0.94[ASN][1000 genomes]
rs2486160	0.94[ASN][1000 genomes]
rs2486162	0.88[ASN][1000 genomes]
rs3011290	0.89[ASN][1000 genomes]
rs3766218	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3766220	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3766221	0.99[ASN][1000 genomes]
rs3766222	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3766223	0.93[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[MKK][hapmap];1.00[ASN][1000 genomes]
rs56771521	0.97[ASN][1000 genomes]
rs57495753	0.97[ASN][1000 genomes]
rs582269	0.96[ASN][1000 genomes]
rs582323	0.94[ASN][1000 genomes]
rs582760	0.96[ASN][1000 genomes]
rs583649	0.94[ASN][1000 genomes]
rs58678760	1.00[ASN][1000 genomes]
rs58920789	0.83[ASN][1000 genomes]
rs59479990	0.97[ASN][1000 genomes]
rs596794	0.96[ASN][1000 genomes]
rs597221	0.96[ASN][1000 genomes]
rs60239027	0.83[ASN][1000 genomes]
rs604233	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs604264	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs611919	0.96[ASN][1000 genomes]
rs629412	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[ASN][1000 genomes]
rs631368	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.94[ASN][1000 genomes]
rs631840	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs636082	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs636122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs636424	0.96[ASN][1000 genomes]
rs648822	0.88[ASN][1000 genomes]
rs654544	0.96[ASN][1000 genomes]
rs655369	0.96[ASN][1000 genomes]
rs657166	0.96[ASN][1000 genomes]
rs669647	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs673134	0.96[ASN][1000 genomes]
rs675731	0.88[ASN][1000 genomes]
rs678466	0.85[ASN][1000 genomes]
rs683585	0.89[ASN][1000 genomes]
rs685862	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs689300	0.96[ASN][1000 genomes]
rs723333	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[ASN][1000 genomes]
rs724309	0.87[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap]
rs72896683	0.88[ASN][1000 genomes]
rs72900715	0.97[ASN][1000 genomes]
rs736188	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[ASN][1000 genomes]
rs9094	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[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	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription 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	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription 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	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47141400-47183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:47143800-47171600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:47154600-47183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:47155600-47169000	Weak transcription	Stomach Mucosa	stomach
5	chr1:47157600-47172200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:47158200-47172000	Weak transcription	Brain Angular Gyrus	brain
7	chr1:47158800-47171000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:47159200-47182800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:47159400-47161400	Weak transcription	HepG2	liver
10	chr1:47159400-47171200	Weak transcription	Right Ventricle	heart
11	chr1:47159400-47172200	Weak transcription	Psoas Muscle	Psoas
12	chr1:47159600-47168200	Weak transcription	HMEC	breast
13	chr1:47160600-47162400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:47160600-47165000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr1:47160600-47165200	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr1:47160600-47165200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:47160600-47165800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:47160600-47169000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:47160600-47169400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:47160600-47173600	Strong transcription	Primary T cells from cord blood	blood
21	chr1:47160600-47174000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:47160600-47181200	Strong transcription	Dnd41	blood
23	chr1:47160800-47161400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:47160800-47162000	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr1:47160800-47162200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:47160800-47162200	Strong transcription	Thymus	Thymus
27	chr1:47160800-47162200	Strong transcription	HUVEC	blood vessel
28	chr1:47160800-47162400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:47160800-47162400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:47160800-47162400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:47160800-47162400	Strong transcription	Spleen	Spleen
32	chr1:47160800-47162400	Strong transcription	A549	lung
33	chr1:47160800-47162600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:47160800-47162600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:47160800-47162600	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr1:47160800-47162600	Strong transcription	Colon Smooth Muscle	Colon
37	chr1:47160800-47162800	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr1:47160800-47162800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:47160800-47162800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:47160800-47162800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:47160800-47162800	Strong transcription	Brain Substantia Nigra	brain
42	chr1:47160800-47162800	Strong transcription	HSMM	muscle
43	chr1:47160800-47162800	Strong transcription	Osteobl	bone
44	chr1:47160800-47163000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:47160800-47163200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:47160800-47163200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:47160800-47163400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:47160800-47163400	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:47160800-47163400	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:47160800-47163400	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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