Variant report

Variant	rs2227617
Chromosome Location	chr1:173874059-173874060
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173837274..173839505-chr1:173873225..173874902,2	MCF-7	breast:
2	chr1:173872208..173874805-chr1:173880498..173882579,2	K562	blood:
3	chr1:173872283..173875090-chr1:173876429..173879185,2	K562	blood:
4	chr1:173866393..173868614-chr1:173873170..173875933,2	K562	blood:
5	chr1:173831886..173836698-chr1:173873878..173876410,4	K562	blood:
6	chr1:173865468..173869830-chr1:173871500..173875883,4	MCF-7	breast:
7	chr1:173873481..173875734-chr1:173878715..173880288,2	K562	blood:
8	chr1:173872649..173875466-chr1:173884584..173887622,3	K562	blood:
9	chr1:173836882..173839099-chr1:173871518..173875909,3	MCF-7	breast:
10	chr1:173826504..173829648-chr1:173870510..173874111,3	K562	blood:
11	chr1:173873065..173875466-chr1:173884584..173886151,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000185278	Chromatin interaction
ENSG00000270084	Chromatin interaction
ENSG00000117601	Chromatin interaction
ENSG00000208317	Chromatin interaction
ENSG00000234741	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs14262	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16846546	0.86[ASW][hapmap];0.88[LWK][hapmap];0.80[YRI][hapmap]
rs16846561	0.88[LWK][hapmap];0.80[YRI][hapmap]
rs16846660	0.85[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap]
rs1885679	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2227602	0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56913226	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57068378	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57652095	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57688313	0.96[AFR][1000 genomes]
rs57740496	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59175258	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60504641	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61083918	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61625780	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6687429	0.92[LWK][hapmap];1.00[MEX][hapmap]

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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173855600-173875400	Weak transcription	NH-A	brain
2	chr1:173855800-173880400	Weak transcription	Thymus	Thymus
3	chr1:173856000-173883000	Weak transcription	Right Ventricle	heart
4	chr1:173856200-173875400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:173856200-173878400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:173856200-173880400	Weak transcription	Psoas Muscle	Psoas
7	chr1:173856400-173876000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:173856400-173880000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:173856600-173881200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:173856600-173907200	Weak transcription	Brain Germinal Matrix	brain
11	chr1:173857000-173883800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:173857400-173880400	Weak transcription	Fetal Brain Female	brain
13	chr1:173857400-173881800	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:173857400-173884400	Weak transcription	HepG2	liver
15	chr1:173857400-173885800	Weak transcription	Fetal Intestine Large	intestine
16	chr1:173857400-173902000	Weak transcription	HSMMtube	muscle
17	chr1:173858200-173902800	Weak transcription	Left Ventricle	heart
18	chr1:173858400-173878600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:173858600-173881400	Weak transcription	Primary B cells from cord blood	blood
20	chr1:173858600-173886800	Weak transcription	Placenta	Placenta
21	chr1:173858800-173876000	Weak transcription	NHLF	lung
22	chr1:173862000-173891600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:173863600-173875800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:173863800-173878800	Weak transcription	Aorta	Aorta
25	chr1:173864000-173875600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:173864200-173878600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:173864600-173878200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr1:173864600-173886600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:173865200-173874600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr1:173866600-173878600	Strong transcription	Liver	Liver
31	chr1:173869000-173880200	Weak transcription	Brain Angular Gyrus	brain
32	chr1:173869200-173880200	Weak transcription	Brain Substantia Nigra	brain
33	chr1:173869800-173877800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:173870000-173880400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:173870000-173898000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:173870200-173876600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:173870200-173880600	Weak transcription	Adipose Nuclei	Adipose
38	chr1:173870400-173887400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:173871200-173908400	Weak transcription	Spleen	Spleen
40	chr1:173871400-173879400	Weak transcription	Colon Smooth Muscle	Colon
41	chr1:173872200-173880200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr1:173872200-173880800	Weak transcription	Fetal Stomach	stomach
43	chr1:173872400-173896200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:173873200-173874400	Strong transcription	Primary T cells from cord blood	blood
45	chr1:173873600-173880600	Weak transcription	Ovary	ovary

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