Variant report

Variant	rs3824734
Chromosome Location	chr10:93999850-93999851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:93969866..93972797-chr10:93997351..93999951,2	MCF-7	breast:
2	chr10:93998891..94002756-chr10:94046633..94048810,3	MCF-7	breast:
3	chr10:93997153..94001150-chr10:94050454..94053150,4	K562	blood:
4	chr10:93993398..93996089-chr10:93999200..94001184,3	K562	blood:
5	chr10:93997118..94002694-chr10:94002870..94008304,8	K562	blood:
6	chr10:93995692..93998257-chr10:93998323..94000901,2	MCF-7	breast:
7	chr10:93998311..94000738-chr10:94062996..94065016,2	K562	blood:
8	chr10:93997685..94001511-chr10:94048071..94053185,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000107864	Chromatin interaction
ENSG00000198060	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10748577	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10748578	0.86[EUR][1000 genomes]
rs10748579	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs10748580	0.83[EUR][1000 genomes]
rs10786029	0.90[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs10786031	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10786033	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10786037	0.96[CEU][hapmap]
rs10882028	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[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];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882042	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1099379	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap]
rs11186914	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11186915	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1229578	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs1229579	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1622656	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs1711849	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1971471	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2253904	0.81[AMR][1000 genomes]
rs2254667	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2255718	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs2265195	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs2488793	0.83[EUR][1000 genomes]
rs2767654	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2771248	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2771253	0.87[EUR][1000 genomes]
rs2771256	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs2771265	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2798254	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs3781229	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4642988	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4933227	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4933228	1.00[CEU][hapmap];0.95[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];0.97[ASN][1000 genomes]
rs4933229	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4933720	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4999831	0.83[EUR][1000 genomes]
rs6583804	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs701846	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7071943	0.85[ASN][1000 genomes]
rs7078559	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[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];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7087501	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[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];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7090737	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7091853	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094433	0.85[EUR][1000 genomes]
rs7897555	0.89[ASN][1000 genomes]
rs7908721	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7914436	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7920520	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs833385	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs855698	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs855699	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs855702	0.86[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs855703	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs855704	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs855707	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs855708	0.81[ASN][1000 genomes]
rs855710	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs913649	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs9943333	0.83[EUR][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	nsv975763	chr10:93822289-94105956	Enhancers Bivalent Enhancer Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1046258	chr10:93866969-94466106	Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3824734	RNLS	cis	parietal	SCAN
rs3824734	RNLS	cis	cerebellum	SCAN
rs3824734	TNKS2	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93997000-94003400	Active TSS	Right Atrium	heart
2	chr10:93997400-94001200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr10:93997400-94003200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr10:93997800-94000000	Flanking Active TSS	NHEK	skin
5	chr10:93997800-94001200	Active TSS	Esophagus	oesophagus
6	chr10:93997800-94002400	Active TSS	Left Ventricle	heart
7	chr10:93998000-94000200	Flanking Active TSS	HMEC	breast
8	chr10:93998000-94001000	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr10:93998000-94001200	Active TSS	Pancreas	Pancrea
10	chr10:93998000-94001400	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr10:93998000-94003400	Active TSS	Psoas Muscle	Psoas
12	chr10:93998200-94000600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr10:93998200-94001200	Active TSS	Ovary	ovary
14	chr10:93998200-94003400	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr10:93998200-94003400	Active TSS	Right Ventricle	heart
16	chr10:93998400-94001000	Active TSS	Fetal Kidney	kidney
17	chr10:93998600-94000200	Active TSS	Primary T cells from cord blood	blood
18	chr10:93998600-94000600	Active TSS	Rectal Smooth Muscle	rectum
19	chr10:93998800-94000000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr10:93998800-94000200	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr10:93998800-94000400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr10:93998800-94000800	Active TSS	Gastric	stomach
23	chr10:93998800-94001000	Active TSS	Brain Hippocampus Middle	brain
24	chr10:93998800-94001200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
25	chr10:93998800-94001400	Active TSS	HSMMtube	muscle
26	chr10:93998800-94003400	Active TSS	Brain Angular Gyrus	brain
27	chr10:93999000-94000000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr10:93999000-94000000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
29	chr10:93999000-94000200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr10:93999000-94000200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr10:93999000-94000200	Active TSS	HepG2	liver
32	chr10:93999000-94000400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
33	chr10:93999000-94000800	Active TSS	Colon Smooth Muscle	Colon
34	chr10:93999000-94001000	Active TSS	Brain Cingulate Gyrus	brain
35	chr10:93999000-94001000	Active TSS	Fetal Intestine Large	intestine
36	chr10:93999000-94001000	Active TSS	Fetal Stomach	stomach
37	chr10:93999000-94001000	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr10:93999000-94001000	Active TSS	Stomach Mucosa	stomach
39	chr10:93999000-94001200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr10:93999000-94001200	Active TSS	Aorta	Aorta
41	chr10:93999000-94001200	Active TSS	Brain Anterior Caudate	brain
42	chr10:93999000-94001200	Active TSS	NHDF-Ad	bronchial
43	chr10:93999000-94001400	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr10:93999200-94000000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr10:93999200-94000000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr10:93999200-94000000	Weak transcription	Fetal Heart	heart
47	chr10:93999200-94000200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
48	chr10:93999200-94000200	Bivalent/Poised TSS	Fetal Thymus	thymus
49	chr10:93999200-94000400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
50	chr10:93999200-94000400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell

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