Variant report

Variant	rs12465295
Chromosome Location	chr2:173346500-173346501
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173345647..173349906-chr2:173350221..173353831,5	K562	blood:
2	chr2:173345156..173347147-chr2:173350221..173352844,2	K562	blood:

Variant related genes	Relation type
ENSG00000091409	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10171775	0.90[EUR][1000 genomes]
rs10174809	0.87[CHB][hapmap]
rs10175670	0.85[JPT][hapmap]
rs10195932	1.00[CEU][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs10197251	0.82[JPT][hapmap]
rs10497381	0.82[JPT][hapmap]
rs10497385	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1076595	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12465442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12467358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12469875	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs12469958	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12474168	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12474995	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12475916	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12476126	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12477247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12477594	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12478465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12619242	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12622044	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12622687	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13383151	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13402061	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1344272	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1574247	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16860377	0.82[JPT][hapmap]
rs16860543	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16860805	1.00[CEU][hapmap]
rs16860809	1.00[CEU][hapmap]
rs2084732	1.00[CEU][hapmap]
rs2178474	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293646	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293649	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2357415	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34094408	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3749148	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3762619	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs3792257	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792260	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3934627	0.85[JPT][hapmap]
rs4281870	0.86[EUR][1000 genomes]
rs4308101	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4480959	0.82[JPT][hapmap]
rs4619573	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs4972515	1.00[CEU][hapmap]
rs56084828	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57957394	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58016698	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58044442	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59020762	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs59610589	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60275829	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60446415	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6718477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755100	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs733331	1.00[CEU][hapmap]
rs7564591	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7564654	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7565216	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7582972	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7591883	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7609465	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173321400-173356000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:173327200-173353200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:173327800-173370800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:173328800-173353400	Weak transcription	Right Ventricle	heart
5	chr2:173329800-173371200	Weak transcription	Hela-S3	cervix
6	chr2:173330200-173350400	Weak transcription	Primary B cells from cord blood	blood
7	chr2:173330400-173360400	Weak transcription	Small Intestine	intestine
8	chr2:173330600-173351400	Weak transcription	Psoas Muscle	Psoas
9	chr2:173330600-173351400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:173330600-173351600	Weak transcription	Brain Anterior Caudate	brain
11	chr2:173330600-173352400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:173330600-173352600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:173330600-173352600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:173330600-173353200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:173330600-173353200	Weak transcription	Aorta	Aorta
16	chr2:173330600-173353400	Weak transcription	Fetal Stomach	stomach
17	chr2:173330600-173371400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:173330600-173372200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:173330600-173373200	Strong transcription	NHEK	skin
20	chr2:173330600-173373400	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:173330600-173373400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:173330600-173373600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:173330600-173374200	Weak transcription	Stomach Mucosa	stomach
24	chr2:173330800-173348200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:173331000-173346600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:173331000-173348400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:173331000-173370000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr2:173331000-173373200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:173331000-173373400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:173331000-173373800	Strong transcription	HMEC	breast
31	chr2:173331200-173372000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:173331400-173370200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:173331600-173348800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:173331800-173348000	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr2:173332400-173351400	Weak transcription	Spleen	Spleen
36	chr2:173334000-173349600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:173335400-173354000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr2:173337800-173360200	Strong transcription	Fetal Thymus	thymus
39	chr2:173338000-173349200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:173341200-173347800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:173342600-173353600	Weak transcription	A549	lung
42	chr2:173343000-173348000	Strong transcription	Esophagus	oesophagus
43	chr2:173343000-173349800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
44	chr2:173343000-173360200	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:173343600-173348000	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr2:173343600-173349000	Weak transcription	Fetal Muscle Leg	muscle
47	chr2:173343600-173349800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
48	chr2:173343800-173351800	Weak transcription	Liver	Liver
49	chr2:173344000-173356000	Weak transcription	Fetal Kidney	kidney
50	chr2:173344200-173348000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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