Variant report

Variant	rs10930542
Chromosome Location	chr2:173164799-173164800
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	chr2:173163058..173164820-chr2:173292652..173294328,2	MCF-7	breast:
2	chr2:173156581..173161480-chr2:173162847..173166156,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226963	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10803872	0.82[AFR][1000 genomes]
rs10930540	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10930541	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10930543	0.82[AFR][1000 genomes]
rs10930544	0.81[AFR][1000 genomes]
rs10930545	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930547	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11674489	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11674629	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11674681	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11677934	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685584	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12475457	0.82[AFR][1000 genomes]
rs12614676	0.82[AFR][1000 genomes]
rs12624040	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13384490	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4429441	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4438453	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4447582	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4450575	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4538169	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4594405	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4619572	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4972477	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4972774	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4972775	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55893326	0.87[EUR][1000 genomes]
rs56239652	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57101510	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7425702	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv3034	chr2:173160295-173200113	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	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:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173151400-173168000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:173161200-173172600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:173161400-173172200	Weak transcription	Right Atrium	heart
4	chr2:173161600-173165800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr2:173162200-173164800	Enhancers	HSMMtube	muscle
6	chr2:173162400-173172600	Weak transcription	Fetal Thymus	thymus
7	chr2:173162800-173165000	Enhancers	Fetal Muscle Leg	muscle
8	chr2:173163200-173164800	Enhancers	Pancreas	Pancrea
9	chr2:173164000-173165000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr2:173164000-173165200	Enhancers	Stomach Mucosa	stomach
11	chr2:173164200-173164800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:173164200-173165000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:173164200-173165000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:173164200-173165000	Enhancers	HSMM	muscle
15	chr2:173164200-173165000	Enhancers	Osteobl	bone
16	chr2:173164200-173165200	Enhancers	HMEC	breast
17	chr2:173164400-173164800	Enhancers	Small Intestine	intestine
18	chr2:173164400-173165000	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr2:173164400-173165000	Enhancers	NHEK	skin
20	chr2:173164400-173165400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr2:173164600-173165000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr2:173164600-173165000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:173164600-173165000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr2:173164600-173165000	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr2:173164600-173165200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:173164600-173165200	Weak transcription	Fetal Lung	lung
27	chr2:173164600-173165200	Enhancers	Monocytes-CD14+_RO01746	blood

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