Variant report

Variant	rs9468375
Chromosome Location	chr6:28392234-28392235
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28390398..28392930-chr6:28395199..28398373,4	K562	blood:
2	chr6:28389572..28392930-chr6:28395042..28397704,3	K562	blood:
3	chr6:28380846..28382983-chr6:28391973..28394917,2	K562	blood:
4	chr6:28370825..28372910-chr6:28390622..28392729,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZSCAN23-1	chr6:28392120-28394123	NONHSAT108462

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10080420	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150715	0.86[ASN][1000 genomes]
rs1150722	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1150723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1150725	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1225600	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12332986	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1600621	0.86[ASN][1000 genomes]
rs1679723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1736892	0.86[ASN][1000 genomes]
rs1778510	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2057295	1.00[EUR][1000 genomes]
rs2108924	1.00[JPT][hapmap]
rs2191036	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2394119	1.00[EUR][1000 genomes]
rs2799076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs28382606	1.00[EUR][1000 genomes]
rs28475822	0.86[ASN][1000 genomes]
rs2859375	1.00[JPT][hapmap]
rs34358978	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34931542	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3757180	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3757183	0.90[ASN][1000 genomes]
rs381493	1.00[EUR][1000 genomes]
rs384399	1.00[EUR][1000 genomes]
rs389603	1.00[EUR][1000 genomes]
rs399558	1.00[EUR][1000 genomes]
rs402426	1.00[EUR][1000 genomes]
rs404343	1.00[EUR][1000 genomes]
rs408255	1.00[EUR][1000 genomes]
rs411538	1.00[EUR][1000 genomes]
rs418898	1.00[EUR][1000 genomes]
rs422089	1.00[EUR][1000 genomes]
rs424426	1.00[EUR][1000 genomes]
rs426922	1.00[EUR][1000 genomes]
rs429875	1.00[EUR][1000 genomes]
rs434636	1.00[EUR][1000 genomes]
rs442174	1.00[EUR][1000 genomes]
rs443924	1.00[EUR][1000 genomes]
rs454746	1.00[EUR][1000 genomes]
rs6456812	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6456817	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6456820	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6899512	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6901001	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6902583	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6908459	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6910120	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6912921	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6918043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6918631	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6922161	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6922302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6923163	1.00[EUR][1000 genomes]
rs6927023	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6929449	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6935589	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6937042	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6938371	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6941222	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7382309	1.00[EUR][1000 genomes]
rs7382583	1.00[EUR][1000 genomes]
rs7752448	1.00[JPT][hapmap]
rs7752721	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7759855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7767897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7773193	1.00[EUR][1000 genomes]
rs911177	1.00[EUR][1000 genomes]
rs9295769	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9295770	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9461450	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9461452	0.86[ASN][1000 genomes]
rs9461453	0.86[ASN][1000 genomes]
rs9461457	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9461464	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9468328	0.86[ASN][1000 genomes]
rs9468335	0.86[ASN][1000 genomes]
rs9468337	0.86[ASN][1000 genomes]
rs9468341	0.86[ASN][1000 genomes]
rs9468384	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9654587	1.00[EUR][1000 genomes];0.93[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	esv1836974	chr6:28376981-28398748	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28371200-28410400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:28383600-28392600	Weak transcription	Brain Germinal Matrix	brain
3	chr6:28383800-28393000	Weak transcription	Fetal Intestine Small	intestine
4	chr6:28384600-28410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:28385400-28402000	Weak transcription	Fetal Kidney	kidney
6	chr6:28385400-28402200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:28385600-28410800	Weak transcription	Lung	lung
8	chr6:28386000-28402200	Weak transcription	Osteobl	bone
9	chr6:28386000-28410400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:28386200-28395800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:28386600-28392800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:28386600-28397800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:28386800-28393600	Weak transcription	Fetal Heart	heart
14	chr6:28386800-28402200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:28387600-28393000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:28387600-28394200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:28387800-28393000	Weak transcription	Fetal Brain Male	brain
18	chr6:28387800-28395400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr6:28387800-28410200	Weak transcription	Brain Angular Gyrus	brain
20	chr6:28388000-28392800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:28388000-28410400	Weak transcription	NHDF-Ad	bronchial
22	chr6:28388400-28393000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:28388400-28399200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr6:28389000-28392600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr6:28389200-28393200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:28389200-28410200	Weak transcription	NHLF	lung
27	chr6:28389400-28393000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:28389400-28403200	Weak transcription	Adipose Nuclei	Adipose
29	chr6:28389400-28410000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:28389600-28398200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:28389600-28409800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr6:28389600-28410200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr6:28389600-28410400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:28389600-28410400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:28389800-28392800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:28389800-28393000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr6:28389800-28410800	Weak transcription	Colonic Mucosa	Colon
38	chr6:28390000-28392400	Strong transcription	Fetal Brain Female	brain
39	chr6:28390000-28393200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:28390200-28392600	Strong transcription	Fetal Lung	lung
41	chr6:28390200-28410400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:28391000-28393000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr6:28391000-28395200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:28391200-28392400	Enhancers	K562	blood
45	chr6:28391400-28392800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:28391400-28402400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr6:28391400-28410400	Weak transcription	Fetal Intestine Large	intestine
48	chr6:28391400-28410800	Weak transcription	Placenta	Placenta
49	chr6:28391600-28392800	Weak transcription	Fetal Muscle Leg	muscle
50	chr6:28391600-28393000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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