Variant report

Variant	rs16860634
Chromosome Location	chr2:173368358-173368359
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DLX2-4	chr2:173368167-173368870	ENSG00000225205.1

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	ITGA6	hsa-miR-30a-5p	chr2:173368356-173368363

Variant related genes	Relation type
ITGA6	miRNA target site

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1001926	1.00[AFR][1000 genomes]
rs10207640	1.00[CEU][hapmap]
rs10207654	1.00[CEU][hapmap]
rs10930559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10930561	0.82[CHB][hapmap]
rs12052253	1.00[CEU][hapmap]
rs12052385	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12053442	1.00[AFR][1000 genomes]
rs12613307	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12615584	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12621278	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12622724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13410475	1.00[CEU][hapmap]
rs13414928	1.00[CEU][hapmap]
rs1530864	0.82[CHB][hapmap]
rs1530865	0.82[CHB][hapmap]
rs1574256	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs1574259	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs16860397	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs16860419	1.00[AFR][1000 genomes]
rs16860426	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs16860438	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16860478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16860513	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16860515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16860643	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860693	0.82[CHB][hapmap]
rs2008518	1.00[AFR][1000 genomes]
rs2178476	1.00[AFR][1000 genomes]
rs2272496	1.00[AFR][1000 genomes]
rs2293645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293647	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2293648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762618	1.00[CEU][hapmap]
rs4405725	1.00[CEU][hapmap]
rs55867175	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56882727	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57244773	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57404607	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs57587465	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59374567	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs59476799	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59970483	0.92[EUR][1000 genomes]
rs60096331	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6730284	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6741759	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6743174	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7591769	0.81[ASN][1000 genomes]
rs9636257	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[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:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173327800-173370800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:173329800-173371200	Weak transcription	Hela-S3	cervix
3	chr2:173330600-173371400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr2:173330600-173372200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:173330600-173373200	Strong transcription	NHEK	skin
6	chr2:173330600-173373400	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:173330600-173373400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:173330600-173373600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:173330600-173374200	Weak transcription	Stomach Mucosa	stomach
10	chr2:173331000-173370000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr2:173331000-173373200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:173331000-173373400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:173331000-173373800	Strong transcription	HMEC	breast
14	chr2:173331200-173372000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:173331400-173370200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:173346000-173370200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:173346000-173370200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:173346000-173370600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:173346400-173371400	Weak transcription	NHLF	lung
20	chr2:173347400-173368600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:173347800-173371600	Weak transcription	Fetal Brain Male	brain
22	chr2:173347800-173376200	Weak transcription	Fetal Heart	heart
23	chr2:173349400-173370400	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr2:173352000-173371400	Weak transcription	Fetal Brain Female	brain
25	chr2:173352000-173374200	Weak transcription	Fetal Lung	lung
26	chr2:173352400-173371400	Weak transcription	Psoas Muscle	Psoas
27	chr2:173353200-173368400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr2:173354000-173370400	Weak transcription	Brain Angular Gyrus	brain
29	chr2:173354200-173369000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:173356400-173379200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:173356600-173371400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:173356600-173375400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:173356800-173369200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:173356800-173369200	Weak transcription	Brain Anterior Caudate	brain
35	chr2:173356800-173374600	Weak transcription	Fetal Kidney	kidney
36	chr2:173356800-173376000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:173356800-173376200	Weak transcription	Brain Substantia Nigra	brain
38	chr2:173357000-173368800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:173357000-173371000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:173357000-173371200	Weak transcription	Ovary	ovary
41	chr2:173357000-173373000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:173357000-173376000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:173357000-173376000	Weak transcription	Aorta	Aorta
44	chr2:173357200-173369200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:173357200-173376600	Weak transcription	Right Ventricle	heart
46	chr2:173357600-173371400	Weak transcription	NH-A	brain
47	chr2:173357600-173376200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:173358000-173376200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:173359200-173371400	Weak transcription	Lung	lung
50	chr2:173359200-173372400	Weak transcription	Brain Hippocampus Middle	brain

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