Variant report

Variant	rs6725309
Chromosome Location	chr2:180021531-180021532
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1048026	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10497533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10497534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11892241	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897308	0.82[YRI][hapmap]
rs11900884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901421	0.82[YRI][hapmap]
rs12105478	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1490997	0.82[YRI][hapmap]
rs16866665	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16866667	0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs16866673	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17363183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17363246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17363323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17363393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17363449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17363603	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs17453976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17454024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17454108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17454150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17454164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17454192	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17454458	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1838872	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2008215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4101465	0.81[ASN][1000 genomes]
rs4499457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58582728	0.84[ASN][1000 genomes]
rs60072979	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61179885	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433759	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433762	0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs6433765	0.83[YRI][hapmap]
rs6433766	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707001	0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs6710100	0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs6723850	0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs6745433	0.93[YRI][hapmap]
rs7598995	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs879539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs930620	0.83[YRI][hapmap];0.82[AFR][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	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv3060	chr2:179990791-180035511	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179973400-180030200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
4	chr2:179980000-180038800	Weak transcription	HMEC	breast
5	chr2:179980000-180056800	Weak transcription	HSMM	muscle
6	chr2:179985000-180025600	Weak transcription	Fetal Intestine Small	intestine
7	chr2:179986600-180030400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:179991600-180043200	Weak transcription	Psoas Muscle	Psoas
9	chr2:179996200-180047600	Weak transcription	NH-A	brain
10	chr2:179998000-180060600	Weak transcription	Right Ventricle	heart
11	chr2:180002400-180030200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:180003200-180039800	Weak transcription	Brain Germinal Matrix	brain
13	chr2:180004800-180046000	Weak transcription	Spleen	Spleen
14	chr2:180005000-180028800	Weak transcription	Hela-S3	cervix
15	chr2:180005600-180040200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:180005600-180044400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:180005600-180044400	Weak transcription	Esophagus	oesophagus
18	chr2:180005800-180030200	Weak transcription	Thymus	Thymus
19	chr2:180005800-180043200	Weak transcription	Fetal Brain Male	brain
20	chr2:180005800-180053600	Weak transcription	Primary T cells from cord blood	blood
21	chr2:180006000-180030600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:180006000-180044600	Weak transcription	Pancreas	Pancrea
23	chr2:180006200-180031400	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:180006200-180031400	Weak transcription	Fetal Brain Female	brain
25	chr2:180006400-180030200	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:180006600-180042000	Weak transcription	Brain Substantia Nigra	brain
27	chr2:180006600-180051000	Weak transcription	HUVEC	blood vessel
28	chr2:180006800-180031600	Weak transcription	Brain Anterior Caudate	brain
29	chr2:180006800-180054600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:180007200-180028600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:180007400-180035200	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:180007400-180035600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:180007400-180042200	Weak transcription	Brain Angular Gyrus	brain
34	chr2:180007400-180043000	Weak transcription	Aorta	Aorta
35	chr2:180007600-180030400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:180007600-180031000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:180007600-180031200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:180008400-180030600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr2:180008400-180042200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr2:180008600-180028400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:180008600-180029400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr2:180008600-180037600	Weak transcription	Fetal Thymus	thymus
43	chr2:180008600-180038400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:180008600-180048400	Weak transcription	Small Intestine	intestine
45	chr2:180009000-180026000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:180011200-180029000	Weak transcription	Dnd41	blood
47	chr2:180011800-180039400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:180012000-180023000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr2:180013200-180044400	Weak transcription	Fetal Kidney	kidney
50	chr2:180014600-180027800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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