Variant report

Variant	rs1541101
Chromosome Location	chr21:40603930-40603931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40602448..40605045-chr21:40605736..40607319,2	K562	blood:
2	chr21:40602604..40604323-chr21:40607724..40609289,2	K562	blood:
3	chr21:40579156..40581832-chr21:40603360..40605633,2	K562	blood:
4	chr21:40589600..40591908-chr21:40602305..40604047,2	K562	blood:
5	chr21:40603008..40605391-chr21:40609514..40611568,2	MCF-7	breast:
6	chr21:40602289..40604074-chr21:40606998..40609550,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229623	Chromatin interaction
ENSG00000237373	Chromatin interaction
ENSG00000185658	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs1011413	0.85[ASN][1000 genomes]
rs10154057	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1041439	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11088471	0.87[CHB][hapmap]
rs11702268	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11910971	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11911822	0.87[ASN][1000 genomes]
rs12626405	0.83[ASN][1000 genomes]
rs13050247	0.93[EUR][1000 genomes]
rs13050584	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13051430	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1541100	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1888487	0.81[ASN][1000 genomes]
rs1963742	0.85[ASN][1000 genomes]
rs1984748	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2026266	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2070867	0.90[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes]
rs2142117	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2150410	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2150412	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2183574	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2183575	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2183576	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2225425	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2236437	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2272576	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2272577	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2272578	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2297258	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2410104	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2410121	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2735310	0.90[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes]
rs2776310	1.00[AFR][1000 genomes]
rs2836969	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs2836971	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs2836975	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs2836982	0.89[CHB][hapmap]
rs28399794	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35909862	0.86[ASN][1000 genomes]
rs3746885	0.83[ASN][1000 genomes]
rs3746886	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3831199	0.80[ASN][1000 genomes]
rs383967	0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs391062	1.00[CEU][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes]
rs413078	1.00[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs425988	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs444130	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs452776	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4816619	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4816620	0.88[ASN][1000 genomes]
rs4816623	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4818004	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818005	0.85[ASN][1000 genomes]
rs4818006	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4818007	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4818011	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4818012	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4818014	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4818015	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs55885019	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56151678	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6517520	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes]
rs6517524	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6517525	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6517528	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs6517529	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6517530	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6517531	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6517532	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6517534	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6517535	0.85[ASN][1000 genomes]
rs6517536	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6517537	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6517539	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6517540	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6517541	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6650847	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66519408	0.93[EUR][1000 genomes]
rs66746936	0.93[EUR][1000 genomes]
rs67212994	0.93[EUR][1000 genomes]
rs67382266	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67649754	0.93[EUR][1000 genomes]
rs68069991	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs68086041	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs68114370	0.93[EUR][1000 genomes]
rs718225	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs719230	0.81[ASN][1000 genomes]
rs726046	0.90[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap]
rs7275773	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7276559	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7276698	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7276774	0.87[CHB][hapmap];0.85[ASN][1000 genomes]
rs7278985	0.85[ASN][1000 genomes]
rs7280149	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7281853	0.89[CHB][hapmap]
rs7282029	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7282724	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7282947	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7283439	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7283652	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8127391	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8127537	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8128118	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8129847	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8130099	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8130774	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8131067	0.86[ASN][1000 genomes]
rs8131091	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8131150	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8131263	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8131307	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8132230	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs914157	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs971229	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs973521	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9974757	0.88[ASN][1000 genomes]
rs9975410	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9975614	0.90[EUR][1000 genomes]
rs9978591	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9978953	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9979547	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9981656	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9982111	0.83[ASN][1000 genomes]
rs9982122	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056683	chr21:40570023-40673210	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv459259	chr21:40571246-40701169	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv587480	chr21:40571246-40701169	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv587481	chr21:40598721-40627020	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1541101	C21orf107	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40563000-40640600	Strong transcription	Placenta	Placenta
2	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr21:40564600-40612600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr21:40565400-40604200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr21:40565400-40612600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr21:40565400-40653600	Strong transcription	Dnd41	blood
12	chr21:40565600-40615000	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr21:40566400-40613200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr21:40569800-40607800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr21:40572000-40636800	Weak transcription	Psoas Muscle	Psoas
17	chr21:40573800-40631000	Weak transcription	Small Intestine	intestine
18	chr21:40578000-40607600	Weak transcription	Aorta	Aorta
19	chr21:40578600-40608000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr21:40578800-40606600	Weak transcription	Brain Substantia Nigra	brain
21	chr21:40580400-40606400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr21:40580600-40607600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr21:40580800-40607200	Weak transcription	Spleen	Spleen
24	chr21:40581400-40635400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr21:40581800-40607200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr21:40582200-40614200	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr21:40582600-40622000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr21:40582800-40654000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr21:40583600-40606800	Weak transcription	NHLF	lung
30	chr21:40588800-40607800	Weak transcription	Right Ventricle	heart
31	chr21:40590000-40605600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr21:40590200-40607200	Weak transcription	NHEK	skin
33	chr21:40590200-40607600	Weak transcription	Brain Hippocampus Middle	brain
34	chr21:40590200-40608000	Weak transcription	Stomach Mucosa	stomach
35	chr21:40590400-40604600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr21:40590600-40607400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr21:40591200-40621600	Strong transcription	Duodenum Mucosa	Duodenum
38	chr21:40591200-40622200	Strong transcription	Liver	Liver
39	chr21:40591400-40625200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr21:40592000-40622400	Strong transcription	K562	blood
41	chr21:40593400-40604800	Strong transcription	Fetal Intestine Large	intestine
42	chr21:40593400-40607200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr21:40593400-40613400	Strong transcription	Fetal Thymus	thymus
44	chr21:40593400-40650800	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr21:40593600-40613200	Strong transcription	Primary T cells from cord blood	blood
46	chr21:40594200-40612200	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr21:40594400-40606600	Weak transcription	A549	lung
48	chr21:40594400-40607800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr21:40595600-40606000	Weak transcription	HMEC	breast
50	chr21:40595800-40604000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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