Variant report

Variant	rs10190530
Chromosome Location	chr2:179238841-179238842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179236261..179239202-chr2:179242335..179244566,2	K562	blood:
2	chr2:179238564..179240183-chr2:179278791..179280896,2	K562	blood:
3	chr2:179230542..179233309-chr2:179237367..179239731,2	K562	blood:
4	chr2:179205985..179207800-chr2:179238644..179240292,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10167053	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12468466	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12468511	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12476608	1.00[ASN][1000 genomes]
rs12615771	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13402046	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1434090	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1434094	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865326	0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61587243	1.00[ASN][1000 genomes]
rs6433724	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706330	0.85[CEU][hapmap];0.98[GIH][hapmap];0.86[LWK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6706354	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710060	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721855	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6724982	0.85[CEU][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6738243	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6738749	0.86[LWK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs6738847	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs733551	0.92[CHB][hapmap];0.96[ASN][1000 genomes]
rs7580795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7607321	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv834466	chr2:179140792-179284778	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10190530	HOXD4	cis	cerebellum	SCAN
rs10190530	CHRNA1	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179183800-179247800	Weak transcription	Psoas Muscle	Psoas
2	chr2:179199000-179241200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr2:179199600-179240400	Weak transcription	Fetal Stomach	stomach
4	chr2:179201800-179240000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:179201800-179240400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:179201800-179240400	Weak transcription	HSMMtube	muscle
7	chr2:179201800-179253600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:179201800-179268200	Weak transcription	HSMM	muscle
9	chr2:179202400-179248000	Weak transcription	NH-A	brain
10	chr2:179209200-179253000	Weak transcription	Esophagus	oesophagus
11	chr2:179210800-179257200	Weak transcription	Pancreas	Pancrea
12	chr2:179215200-179248800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:179215600-179239800	Weak transcription	Brain Anterior Caudate	brain
14	chr2:179217400-179240400	Weak transcription	Aorta	Aorta
15	chr2:179217400-179248400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:179217600-179239600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:179217600-179241800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:179217800-179239000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:179218200-179240000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:179219000-179248000	Weak transcription	Left Ventricle	heart
21	chr2:179224800-179239800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:179225000-179257800	Weak transcription	Lung	lung
23	chr2:179226600-179257200	Weak transcription	Gastric	stomach
24	chr2:179227000-179240600	Weak transcription	Brain Angular Gyrus	brain
25	chr2:179227600-179239600	Weak transcription	Liver	Liver
26	chr2:179228400-179239600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:179228600-179239200	Weak transcription	NHEK	skin
28	chr2:179228800-179247200	Weak transcription	HMEC	breast
29	chr2:179229600-179240800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:179232000-179243800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:179232000-179254200	Weak transcription	Hela-S3	cervix
32	chr2:179232800-179240400	Weak transcription	Fetal Brain Female	brain
33	chr2:179233000-179248200	Weak transcription	Fetal Brain Male	brain
34	chr2:179233200-179240400	Weak transcription	Ovary	ovary
35	chr2:179235600-179251600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr2:179237400-179252200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:179237800-179241000	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:179238400-179247600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:179238400-179251400	Weak transcription	Fetal Intestine Large	intestine
40	chr2:179238600-179239200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:179238600-179242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:179238600-179242600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:179238600-179247800	Weak transcription	Brain Hippocampus Middle	brain

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