Variant report

Variant	rs2576056
Chromosome Location	chr18:44675462-44675463
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:44673432..44675834-chr18:44691617..44693277,2	MCF-7	breast:
2	chr18:44675372..44679287-chr18:44700113..44704114,10	MCF-7	breast:
3	chr18:44664428..44666267-chr18:44672303..44675573,3	K562	blood:
4	chr18:44656520..44659372-chr18:44673623..44675752,2	K562	blood:
5	chr18:44663118..44666144-chr18:44673724..44676472,4	K562	blood:

Variant related genes	Relation type
ENSG00000267228	Chromatin interaction
ENSG00000134049	Chromatin interaction
ENSG00000267800	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11663321	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12960378	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12960444	0.85[EUR][1000 genomes]
rs12963648	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12964465	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17785419	0.85[CEU][hapmap]
rs2251948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277717	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2461247	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2571001	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571009	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2571016	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2576030	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2576031	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576053	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2576060	0.96[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2635040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635041	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2635042	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2635043	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635045	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2635046	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2635047	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2635049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635050	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668779	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2684818	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2684820	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684822	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2684825	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684826	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684837	0.88[CEU][hapmap]
rs28693565	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28702976	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2932126	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3816125	0.96[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7242978	0.96[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7504798	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9304341	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9960264	0.96[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][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	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv833640	chr18:44552276-44714872	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv909612	chr18:44560875-44681485	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv576819	chr18:44602249-44677627	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv909613	chr18:44644530-44690107	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44629200-44675800	Weak transcription	HUVEC	blood vessel
2	chr18:44632400-44675800	Weak transcription	Stomach Mucosa	stomach
3	chr18:44640600-44675600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr18:44641600-44675800	Weak transcription	Lung	lung
5	chr18:44641800-44675800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr18:44641800-44675800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr18:44647800-44675800	Weak transcription	Ovary	ovary
8	chr18:44661200-44675800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr18:44661400-44675600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr18:44661600-44675600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr18:44661600-44675800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr18:44662200-44675800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr18:44662800-44675600	Weak transcription	Brain Angular Gyrus	brain
14	chr18:44662800-44675600	Weak transcription	Fetal Muscle Leg	muscle
15	chr18:44662800-44675600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr18:44662800-44675800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr18:44662800-44675800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr18:44662800-44675800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr18:44662800-44675800	Weak transcription	Brain Anterior Caudate	brain
20	chr18:44662800-44675800	Weak transcription	Placenta	Placenta
21	chr18:44663000-44675600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr18:44663200-44675600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr18:44663400-44675600	Weak transcription	NH-A	brain
24	chr18:44663400-44676000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr18:44663600-44675600	Weak transcription	Fetal Stomach	stomach
26	chr18:44663600-44675600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr18:44663600-44675800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr18:44663600-44675800	Weak transcription	Esophagus	oesophagus
29	chr18:44663600-44675800	Weak transcription	Fetal Intestine Large	intestine
30	chr18:44663600-44675800	Weak transcription	Gastric	stomach
31	chr18:44663600-44675800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr18:44663600-44675800	Weak transcription	Spleen	Spleen
33	chr18:44663600-44675800	Weak transcription	HSMM	muscle
34	chr18:44663800-44675600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr18:44663800-44675800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr18:44663800-44675800	Weak transcription	Fetal Kidney	kidney
37	chr18:44663800-44675800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr18:44664000-44675600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr18:44664000-44675800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr18:44666200-44675800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr18:44668400-44675600	Weak transcription	Right Atrium	heart
42	chr18:44671200-44675800	Weak transcription	Left Ventricle	heart
43	chr18:44671200-44675800	Weak transcription	Pancreas	Pancrea
44	chr18:44671600-44675600	Weak transcription	Right Ventricle	heart
45	chr18:44671600-44675800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr18:44673000-44676000	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr18:44673200-44675800	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr18:44673400-44675600	Weak transcription	Fetal Brain Female	brain
49	chr18:44673600-44675600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr18:44673800-44675600	Weak transcription	Fetal Thymus	thymus

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