Variant report

Variant	rs7425380
Chromosome Location	chr2:173198175-173198176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12996815	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35427086	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4246620	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4290625	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4350710	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4395225	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4487062	0.80[ASN][1000 genomes]
rs4972502	0.80[ASN][1000 genomes]
rs6433351	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6433354	0.80[ASN][1000 genomes]
rs6714434	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6715062	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719962	0.80[ASN][1000 genomes]
rs6723279	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6728360	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6729987	0.80[ASN][1000 genomes]
rs6757748	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7577264	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7583083	0.80[ASN][1000 genomes]
rs7594561	0.82[CHB][hapmap]

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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173195200-173199000	Weak transcription	Colonic Mucosa	Colon
2	chr2:173195400-173199800	Weak transcription	Lung	lung
3	chr2:173195400-173199800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:173195400-173204000	Weak transcription	Left Ventricle	heart
5	chr2:173195400-173204000	Weak transcription	Right Ventricle	heart
6	chr2:173195800-173199600	Weak transcription	Stomach Mucosa	stomach
7	chr2:173196000-173199600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:173196400-173198400	Enhancers	Pancreas	Pancrea
9	chr2:173196800-173198800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:173197200-173198600	Enhancers	Fetal Thymus	thymus
11	chr2:173197200-173198800	Enhancers	Fetal Muscle Leg	muscle
12	chr2:173197400-173198600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:173197400-173198600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:173197400-173198800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr2:173197400-173198800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:173197600-173198200	Enhancers	Brain Cingulate Gyrus	brain
17	chr2:173197600-173198400	Enhancers	Brain Substantia Nigra	brain
18	chr2:173197600-173204000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:173197600-173204400	Weak transcription	Thymus	Thymus
20	chr2:173197800-173198200	Enhancers	Psoas Muscle	Psoas
21	chr2:173197800-173198400	Enhancers	Brain Anterior Caudate	brain
22	chr2:173197800-173198600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:173197800-173198600	Enhancers	Brain Hippocampus Middle	brain
24	chr2:173197800-173198600	Enhancers	Fetal Intestine Small	intestine
25	chr2:173197800-173198600	Enhancers	Fetal Lung	lung
26	chr2:173197800-173198600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr2:173197800-173204000	Enhancers	Duodenum Mucosa	Duodenum
28	chr2:173198000-173198400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:173198000-173198400	Enhancers	Fetal Intestine Large	intestine
30	chr2:173198000-173198400	Enhancers	Small Intestine	intestine
31	chr2:173198000-173198400	Enhancers	Spleen	Spleen
32	chr2:173198000-173198400	Weak transcription	HSMMtube	muscle
33	chr2:173198000-173199800	Weak transcription	Gastric	stomach
34	chr2:173198000-173200400	Enhancers	HepG2	liver

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