Variant report

Variant	rs7552953
Chromosome Location	chr1:225658765-225658766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225649550..225651644-chr1:225657315..225659303,2	MCF-7	breast:
2	chr1:225658101..225659665-chr1:226308804..226311081,2	K562	blood:
3	chr1:225657432..225660259-chr1:225660834..225662970,2	K562	blood:
4	chr1:225646024..225648970-chr1:225656905..225658780,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC092811.1-1	chr1:225657547-225659222	XLOC_000585

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10799312	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10915836	0.86[ASN][1000 genomes]
rs12032961	0.85[ASN][1000 genomes]
rs12124353	0.83[AMR][1000 genomes]
rs12742313	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2039620	0.82[ASN][1000 genomes]
rs3766930	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3856157	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893032	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233220	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4554690	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6692054	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6702641	0.86[ASN][1000 genomes]
rs7522622	0.83[ASN][1000 genomes]
rs7527014	0.83[ASN][1000 genomes]
rs7536925	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7548473	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7550784	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv873227	chr1:225656388-225687981	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv8880	chr1:225656408-225687710	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv826842	chr1:225658062-225686586	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225649800-225662600	Weak transcription	Pancreas	Pancrea
2	chr1:225651400-225662400	Weak transcription	Fetal Brain Male	brain
3	chr1:225653600-225662400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:225653600-225662400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:225653800-225659600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:225655400-225662400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:225655600-225658800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:225655600-225677000	Weak transcription	Right Atrium	heart
9	chr1:225655800-225661200	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:225655800-225661800	Weak transcription	Spleen	Spleen
11	chr1:225655800-225662000	Weak transcription	Right Ventricle	heart
12	chr1:225656000-225659200	Enhancers	Fetal Muscle Leg	muscle
13	chr1:225656200-225659800	Enhancers	Stomach Smooth Muscle	stomach
14	chr1:225656400-225660000	Enhancers	Fetal Thymus	thymus
15	chr1:225656400-225662400	Weak transcription	Liver	Liver
16	chr1:225656400-225662600	Weak transcription	Thymus	Thymus
17	chr1:225656600-225661800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:225656600-225662000	Weak transcription	Lung	lung
19	chr1:225656600-225662600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:225656800-225661000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:225656800-225662400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr1:225656800-225662800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:225656800-225663000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:225657000-225661200	Weak transcription	Primary T cells from cord blood	blood
25	chr1:225657000-225662000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:225657000-225662400	Weak transcription	Primary B cells from cord blood	blood
27	chr1:225657000-225662400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:225657200-225660800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr1:225657200-225660800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:225657200-225661000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:225657200-225661000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:225657200-225661200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:225657200-225662400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:225657400-225660800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr1:225657400-225660800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:225657400-225660800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr1:225657400-225662000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:225657600-225662400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:225657800-225659000	Enhancers	Colon Smooth Muscle	Colon
40	chr1:225658000-225658800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr1:225658000-225659000	Enhancers	Rectal Smooth Muscle	rectum
42	chr1:225658400-225659600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:225658600-225660000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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