Variant report

Variant	rs4933720
Chromosome Location	chr10:94061431-94061432
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	chr10:94051034..94053715-chr10:94061317..94064241,2	K562	blood:
2	chr10:94054680..94057540-chr10:94060571..94063185,3	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10748577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10748578	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10748579	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10748580	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10786029	0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs10786031	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10786033	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10786037	0.96[CEU][hapmap]
rs10882028	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs10882034	0.80[LWK][hapmap]
rs10882042	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11186872	0.80[LWK][hapmap]
rs11186914	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11186915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971471	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2245994	0.86[ASN][1000 genomes]
rs2253904	0.95[ASN][1000 genomes]
rs2254667	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255718	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs2265195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2488793	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2771248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2771253	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2771256	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs2771265	0.95[ASN][1000 genomes]
rs2798254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3781229	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3824734	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]
rs4933227	0.88[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs4933228	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4933229	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4999831	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs701846	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs7078559	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs7087501	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs7090737	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7091853	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7094433	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7908721	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7914436	0.85[ASN][1000 genomes]
rs7920520	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs855699	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs855702	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs855704	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs855707	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs913649	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9943333	0.90[EUR][1000 genomes];0.85[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4933720	RNLS	cis	cerebellum	SCAN
rs4933720	RNLS	cis	parietal	SCAN
rs4933720	TPBG	trans	lymphoblastoid	seeQTL
rs4933720	TNKS2	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94052000-94111800	Weak transcription	Gastric	stomach
2	chr10:94052200-94065800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr10:94052200-94071000	Weak transcription	Fetal Intestine Large	intestine
4	chr10:94052200-94109400	Weak transcription	Esophagus	oesophagus
5	chr10:94052400-94062800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr10:94052400-94063200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr10:94052400-94063200	Weak transcription	Brain Anterior Caudate	brain
8	chr10:94052400-94070800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr10:94052400-94080600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:94052400-94101200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr10:94052400-94101600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr10:94052400-94108800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr10:94052400-94114600	Weak transcription	Colonic Mucosa	Colon
14	chr10:94052600-94061800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr10:94052600-94062200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:94052600-94063200	Weak transcription	Brain Substantia Nigra	brain
17	chr10:94052600-94063600	Weak transcription	Brain Angular Gyrus	brain
18	chr10:94052600-94065200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr10:94052600-94068200	Weak transcription	Small Intestine	intestine
20	chr10:94052600-94070800	Weak transcription	NHDF-Ad	bronchial
21	chr10:94052600-94071600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr10:94052600-94077200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr10:94052600-94102000	Weak transcription	NHLF	lung
24	chr10:94052600-94109400	Weak transcription	HSMMtube	muscle
25	chr10:94052800-94063000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr10:94052800-94063000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr10:94052800-94063200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr10:94052800-94063200	Weak transcription	Colon Smooth Muscle	Colon
29	chr10:94052800-94063800	Weak transcription	Adipose Nuclei	Adipose
30	chr10:94052800-94072000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr10:94052800-94072800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr10:94052800-94087400	Weak transcription	K562	blood
33	chr10:94052800-94088600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr10:94053000-94063000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr10:94053000-94063600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr10:94053000-94070800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr10:94053200-94062200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr10:94053200-94062600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr10:94053200-94063000	Weak transcription	Brain Germinal Matrix	brain
40	chr10:94053200-94071400	Weak transcription	HMEC	breast
41	chr10:94053200-94074600	Weak transcription	Brain Hippocampus Middle	brain
42	chr10:94053200-94086800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr10:94053400-94109400	Weak transcription	Fetal Brain Male	brain
44	chr10:94054000-94063600	Weak transcription	Fetal Heart	heart
45	chr10:94054200-94063000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr10:94054200-94063000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr10:94054400-94061800	Strong transcription	Fetal Stomach	stomach
48	chr10:94054400-94062000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr10:94054400-94062600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr10:94054400-94062600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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