Variant report

Variant	rs2776311
Chromosome Location	chr21:40716885-40716886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
2	21:40712819-40717370..21:40748850-40752541	GM12878	blood:
3	chr21:40716662..40723444-chr21:40748337..40754328,16	MCF-7	breast:
4	chr21:40716442..40724032-chr21:40756185..40762223,18	K562	blood:
5	chr21:40652004..40654564-chr21:40716456..40719134,2	MCF-7	breast:
6	chr21:40716079..40725440-chr21:40756737..40764615,26	K562	blood:

Variant related genes	Relation type
ENSG00000182093	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000238141	Chromatin interaction
ENSG00000185658	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1888490	0.82[CHB][hapmap]
rs2026267	0.86[YRI][hapmap]
rs2239384	0.83[JPT][hapmap]
rs2249666	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2297255	0.81[CHB][hapmap]
rs2735306	0.86[YRI][hapmap]
rs2735307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2776306	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776307	0.86[YRI][hapmap]
rs2776309	0.86[YRI][hapmap]
rs2776312	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836936	0.81[CHB][hapmap]
rs2836937	0.82[CHB][hapmap]
rs2836941	0.81[CHB][hapmap]
rs2836946	0.81[CHB][hapmap]
rs2836947	0.82[CHB][hapmap]
rs2836962	0.82[CHB][hapmap]
rs2836963	0.82[CHB][hapmap]
rs2836970	0.82[CHB][hapmap]
rs2836976	0.82[CHB][hapmap]
rs2836978	0.82[CHB][hapmap]
rs2836979	0.81[CHB][hapmap]
rs2836992	0.83[JPT][hapmap]
rs2854727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2989329	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3167757	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs379291	0.82[CHB][hapmap]
rs420888	0.81[CHB][hapmap]
rs4817997	0.82[CHB][hapmap]
rs4818027	0.83[JPT][hapmap]
rs6517516	0.81[CHB][hapmap]
rs6517517	0.81[CHB][hapmap]
rs6517522	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs7278048	0.82[CHB][hapmap]
rs7281540	0.81[CHB][hapmap]
rs741795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8128901	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8128919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8129303	0.90[AFR][1000 genomes]
rs8129850	0.82[CHB][hapmap]
rs8132993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[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]
rs914156	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9305669	0.81[CHB][hapmap]
rs997146	0.81[CHB][hapmap]
rs9979691	0.81[CHB][hapmap]
rs9980890	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9981595	0.80[CHB][hapmap]

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	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv1059420	chr21:40684295-40745952	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv587483	chr21:40686327-40718161	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2776311	C21orf107	cis	multi-tissue	Pritchard
rs2776311	PSMG1	cis	Artery Tibial	GTEx
rs2776311	HMGN1	cis	multi-tissue	Pritchard
rs2776311	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs2776311	BRWD1	cis	Temporal Cortex	GTEx
rs2776311	DSCR2	cis	normal skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40692400-40718400	Weak transcription	Right Atrium	heart
2	chr21:40704000-40719600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr21:40704600-40717200	Weak transcription	Right Ventricle	heart
4	chr21:40704600-40719600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr21:40711800-40719600	Weak transcription	Pancreas	Pancrea
6	chr21:40712000-40717200	Strong transcription	Fetal Stomach	stomach
7	chr21:40712200-40718800	Strong transcription	Fetal Muscle Trunk	muscle
8	chr21:40712600-40717000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr21:40712600-40717000	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr21:40712600-40717000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr21:40712600-40717000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr21:40712600-40717000	Strong transcription	Duodenum Mucosa	Duodenum
13	chr21:40712600-40717200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr21:40712600-40717400	Strong transcription	Fetal Intestine Large	intestine
15	chr21:40712600-40717400	Strong transcription	Fetal Thymus	thymus
16	chr21:40712600-40717400	Strong transcription	Osteobl	bone
17	chr21:40712600-40717600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr21:40712600-40717600	Strong transcription	Fetal Muscle Leg	muscle
19	chr21:40712600-40717600	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr21:40712600-40717600	Strong transcription	Thymus	Thymus
21	chr21:40712600-40718200	Strong transcription	HSMM	muscle
22	chr21:40712800-40717000	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr21:40712800-40717000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr21:40712800-40717000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr21:40712800-40717000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr21:40712800-40717000	Strong transcription	Fetal Kidney	kidney
27	chr21:40712800-40717000	Strong transcription	HMEC	breast
28	chr21:40712800-40717200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr21:40712800-40717200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr21:40712800-40717400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr21:40712800-40717400	Strong transcription	Liver	Liver
32	chr21:40712800-40717600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr21:40712800-40717600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr21:40712800-40717600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr21:40712800-40717600	Strong transcription	A549	lung
36	chr21:40712800-40717800	Strong transcription	Primary B cells from cord blood	blood
37	chr21:40712800-40717800	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr21:40712800-40718400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr21:40712800-40718600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr21:40712800-40719200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr21:40712800-40719200	Strong transcription	Placenta	Placenta
42	chr21:40713000-40717000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr21:40713000-40717000	Strong transcription	GM12878-XiMat	blood
44	chr21:40713000-40717000	Strong transcription	K562	blood
45	chr21:40713000-40717400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr21:40713000-40718800	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr21:40713200-40717000	Strong transcription	HUVEC	blood vessel
48	chr21:40713200-40717200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr21:40713200-40717400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr21:40713200-40717600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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