Variant report

Variant	rs1804429
Chromosome Location	chr10:44865841-44865842
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:44856118..44857833-chr10:44865837..44868542,2	K562	blood:
2	chr10:44860292..44861820-chr10:44864843..44866905,2	MCF-7	breast:
3	chr10:44864860..44867603-chr10:44877581..44881069,3	MCF-7	breast:

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	CXCL12	hsa-miR-23a-3p	chr10:44865821-44865842

Variant related genes	Relation type
ENSG00000107562	Chromatin interaction
CXCL12	miRNA target site

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1029153	0.80[YRI][hapmap]
rs1065297	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900028	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs10900031	1.00[CHB][hapmap];1.00[JPT][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]
rs11239016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs11239020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11239021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs11239032	0.94[ASN][1000 genomes]
rs12258838	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[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]
rs12357238	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17540465	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17878782	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17881412	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17881729	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17887234	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1804430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1889401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1889402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2522	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2760669	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839696	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[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]
rs4948878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59675227	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60357795	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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	nsv1038511	chr10:44596885-44870030	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1054649	chr10:44848921-44889713	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44838600-44867400	Weak transcription	Spleen	Spleen
2	chr10:44848400-44867400	Weak transcription	Adipose Nuclei	Adipose
3	chr10:44848400-44867600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr10:44849400-44869000	Weak transcription	Right Ventricle	heart
5	chr10:44850600-44877600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr10:44854200-44867200	Weak transcription	Colon Smooth Muscle	Colon
7	chr10:44854400-44869000	Weak transcription	Brain Substantia Nigra	brain
8	chr10:44858800-44866600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr10:44859000-44871800	Weak transcription	Psoas Muscle	Psoas
10	chr10:44860000-44879000	Weak transcription	Gastric	stomach
11	chr10:44860200-44868800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr10:44861400-44869200	Weak transcription	Colonic Mucosa	Colon
13	chr10:44862000-44866400	Genic enhancers	Fetal Muscle Leg	muscle
14	chr10:44862200-44866400	Weak transcription	Brain Germinal Matrix	brain
15	chr10:44863000-44867400	Weak transcription	Pancreas	Pancrea
16	chr10:44863200-44869400	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr10:44863600-44866400	Enhancers	Fetal Lung	lung
18	chr10:44864400-44866200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr10:44864600-44866000	Enhancers	H9 Cell Line	embryonic stem cell
20	chr10:44864600-44866800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr10:44864600-44868000	Weak transcription	NHLF	lung
22	chr10:44864600-44871600	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr10:44864600-44876200	Weak transcription	Brain Anterior Caudate	brain
24	chr10:44864600-44876800	Strong transcription	Fetal Stomach	stomach
25	chr10:44864800-44866400	Enhancers	NHDF-Ad	bronchial
26	chr10:44864800-44877800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr10:44865000-44866000	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr10:44865000-44866200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr10:44865000-44867400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr10:44865000-44873000	Weak transcription	Esophagus	oesophagus
31	chr10:44865200-44866200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr10:44865200-44866200	Strong transcription	Ovary	ovary
33	chr10:44865200-44866200	Genic enhancers	Osteobl	bone
34	chr10:44865200-44868600	Strong transcription	Fetal Muscle Trunk	muscle
35	chr10:44865400-44866000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr10:44865400-44866000	Weak transcription	Left Ventricle	heart
37	chr10:44865400-44867400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr10:44865400-44867400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr10:44865400-44867400	Weak transcription	Aorta	Aorta
40	chr10:44865400-44867400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr10:44865400-44867800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr10:44865400-44876200	Weak transcription	Right Atrium	heart
43	chr10:44865600-44866000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr10:44865600-44866200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr10:44865600-44868000	Weak transcription	Fetal Kidney	kidney
46	chr10:44865600-44878000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr10:44865800-44866000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr10:44865800-44866200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr10:44865800-44866200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr10:44865800-44866400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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