Variant report

Variant	rs10890407
Chromosome Location	chr1:47069730-47069731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47054632..47056967-chr1:47067428..47069828,2	K562	blood:
2	chr1:47069390..47072755-chr1:47079314..47082367,4	MCF-7	breast:
3	chr1:47053775..47056193-chr1:47067460..47069823,2	MCF-7	breast:
4	chr1:47068429..47072503-chr1:47081068..47085092,4	MCF-7	breast:
5	chr1:47068203..47069866-chr1:47187301..47190738,3	MCF-7	breast:
6	chr1:47033343..47035201-chr1:47067108..47069992,2	K562	blood:
7	chr1:47041717..47044206-chr1:47067000..47069818,2	K562	blood:

Variant related genes	Relation type
ENSG00000079277	Chromatin interaction
ENSG00000142961	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10890406	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10890408	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11211319	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211320	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211323	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211324	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11211325	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11211326	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11211327	0.86[EUR][1000 genomes]
rs12022855	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12136479	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1258012	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35494693	0.86[EUR][1000 genomes]
rs36058295	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4660357	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4660947	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6671527	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6687832	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6704020	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7526249	0.98[EUR][1000 genomes]
rs7526328	0.97[EUR][1000 genomes]
rs942083	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs956526	0.96[EUR][1000 genomes]
rs956527	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1008246	chr1:47007844-47069845	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv870392	chr1:47040676-47095097	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47068400-47069800	Flanking Active TSS	Fetal Thymus	thymus
2	chr1:47068400-47069800	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr1:47068600-47069800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr1:47068600-47069800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
5	chr1:47068800-47070400	Active TSS	HSMM	muscle
6	chr1:47068800-47070600	Active TSS	NHLF	lung
7	chr1:47069000-47069800	Flanking Active TSS	Fetal Muscle Trunk	muscle
8	chr1:47069000-47069800	Flanking Active TSS	HUVEC	blood vessel
9	chr1:47069000-47070200	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr1:47069000-47070200	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr1:47069000-47070400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:47069000-47070400	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr1:47069000-47070400	Active TSS	Colonic Mucosa	Colon
14	chr1:47069000-47070400	Active TSS	A549	lung
15	chr1:47069000-47070800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:47069000-47071200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:47069200-47069800	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr1:47069200-47069800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:47069200-47069800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:47069200-47070000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:47069200-47070000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:47069200-47070000	Active TSS	Small Intestine	intestine
23	chr1:47069200-47070200	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr1:47069200-47070200	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr1:47069200-47070400	Active TSS	H9 Cell Line	embryonic stem cell
26	chr1:47069200-47070400	Active TSS	Colon Smooth Muscle	Colon
27	chr1:47069200-47070400	Active TSS	Fetal Kidney	kidney
28	chr1:47069200-47070600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:47069200-47070600	Active TSS	Aorta	Aorta
30	chr1:47069200-47070600	Active TSS	Ovary	ovary
31	chr1:47069200-47070800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:47069400-47069800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr1:47069400-47069800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
34	chr1:47069400-47069800	Bivalent/Poised TSS	HepG2	liver
35	chr1:47069400-47070000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:47069400-47070000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:47069400-47070000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:47069400-47070000	Active TSS	Placenta Amnion	Placenta Amnion
39	chr1:47069400-47070000	Active TSS	Stomach Mucosa	stomach
40	chr1:47069400-47070200	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr1:47069400-47070200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:47069400-47070200	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr1:47069400-47070200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:47069400-47070200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:47069400-47070200	Active TSS	Liver	Liver
46	chr1:47069400-47070200	Active TSS	Fetal Intestine Large	intestine
47	chr1:47069400-47070200	Active TSS	Gastric	stomach
48	chr1:47069400-47070200	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr1:47069400-47070200	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr1:47069400-47070200	Active TSS	NHEK	skin

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