Variant report

Variant	rs2299816
Chromosome Location	chr21:45486216-45486217
allele	A/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45483486..45486444-chr21:45498121..45500781,3	K562	blood:
2	chr21:45462776..45465739-chr21:45484700..45487223,2	K562	blood:
3	chr21:45485665..45487359-chr21:45490550..45492983,2	K562	blood:
4	chr21:45449259..45451430-chr21:45484484..45487019,2	K562	blood:
5	chr21:45483406..45486402-chr21:45486575..45488365,2	MCF-7	breast:
6	chr21:45486005..45488268-chr21:45490821..45492740,2	MCF-7	breast:
7	chr21:45430698..45433367-chr21:45485628..45489099,4	MCF-7	breast:
8	chr21:45483221..45485092-chr21:45485897..45487592,2	MCF-7	breast:
9	chr21:45476652..45480295-chr21:45485072..45489102,4	MCF-7	breast:
10	chr21:45485859..45488146-chr21:45491483..45493752,2	K562	blood:
11	chr21:45473377..45479336-chr21:45481371..45487468,11	K562	blood:

No data

Variant related genes	Relation type
ENSG00000160218	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1051981	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs1131999	0.81[CEU][hapmap]
rs13047030	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13047214	0.86[ASN][1000 genomes]
rs13048791	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13050630	0.88[EUR][1000 genomes]
rs17004630	0.90[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs2006694	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs2020948	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs2071152	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs2071154	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2156428	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs2187313	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2238704	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs2238705	0.80[EUR][1000 genomes]
rs2238706	0.82[EUR][1000 genomes]
rs2238707	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs2238708	0.87[EUR][1000 genomes]
rs2238710	0.88[EUR][1000 genomes]
rs2238711	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs2238712	0.87[EUR][1000 genomes]
rs2243348	0.81[EUR][1000 genomes]
rs2245372	0.88[EUR][1000 genomes]
rs2245380	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs2245386	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs2245462	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs2245759	0.82[EUR][1000 genomes]
rs2247400	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs2255016	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2255955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2256392	0.82[EUR][1000 genomes]
rs2256441	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs2276532	1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs2277805	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299812	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs2299813	0.82[EUR][1000 genomes]
rs2299817	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2299820	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs2838464	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2838467	0.88[EUR][1000 genomes]
rs2838468	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs2838469	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2838472	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs2838476	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs2838477	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs2838478	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2838480	0.82[EUR][1000 genomes]
rs2838481	0.88[EUR][1000 genomes]
rs2838483	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs2838485	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs2838507	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs2838508	0.85[JPT][hapmap]
rs2838509	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs28385580	0.86[ASN][1000 genomes]
rs2850154	0.93[JPT][hapmap]
rs35524612	0.86[ASN][1000 genomes]
rs35610725	0.88[EUR][1000 genomes]
rs3788097	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs3788098	0.84[EUR][1000 genomes]
rs3788101	0.80[EUR][1000 genomes]
rs3788102	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788104	0.90[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3788108	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs4818878	0.82[EUR][1000 genomes]
rs4818886	0.90[CHB][hapmap]
rs4819361	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4819362	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4819366	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs4819375	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs59675192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62226688	0.87[ASN][1000 genomes]
rs7275722	0.84[ASN][1000 genomes]
rs7276709	0.86[ASN][1000 genomes]
rs7279727	0.88[EUR][1000 genomes]
rs7282324	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs729882	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs7676	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs8126754	0.87[EUR][1000 genomes]
rs8126958	0.81[CEU][hapmap]
rs8129971	0.82[EUR][1000 genomes]
rs885872	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs915878	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs9306169	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9306171	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs9306174	0.88[EUR][1000 genomes]
rs965733	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs968713	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs9974165	0.82[EUR][1000 genomes]
rs9975708	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs9981257	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs9982663	0.87[EUR][1000 genomes]
rs9985064	0.90[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv459293	chr21:45415913-45555079	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv587721	chr21:45415913-45555079	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1064549	chr21:45446358-45493720	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1064420	chr21:45460089-45814986	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv544472	chr21:45460089-45814986	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	nsv432155	chr21:45479055-45772388	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
9	nsv913890	chr21:45482950-45603746	Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2299816	PWP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45445400-45509400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr21:45446400-45502200	Weak transcription	Fetal Heart	heart
3	chr21:45451000-45494400	Weak transcription	Fetal Brain Male	brain
4	chr21:45465800-45487800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr21:45468400-45502400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr21:45468800-45502600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr21:45469400-45487000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr21:45469400-45502000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr21:45471400-45487000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr21:45471800-45495400	Strong transcription	Fetal Muscle Leg	muscle
11	chr21:45471800-45502200	Strong transcription	Fetal Intestine Small	intestine
12	chr21:45472000-45494200	Weak transcription	Psoas Muscle	Psoas
13	chr21:45472000-45502600	Strong transcription	Duodenum Mucosa	Duodenum
14	chr21:45472400-45491200	Strong transcription	Fetal Intestine Large	intestine
15	chr21:45472600-45504400	Strong transcription	Fetal Stomach	stomach
16	chr21:45472800-45503800	Strong transcription	Liver	Liver
17	chr21:45473000-45526600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr21:45475000-45493000	Strong transcription	Fetal Muscle Trunk	muscle
19	chr21:45475000-45502600	Weak transcription	Right Atrium	heart
20	chr21:45475200-45487600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr21:45475200-45494000	Weak transcription	Fetal Kidney	kidney
22	chr21:45475600-45491200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr21:45476200-45487600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr21:45478200-45487000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr21:45479800-45491200	Weak transcription	Small Intestine	intestine
26	chr21:45480000-45486800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr21:45481400-45487600	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr21:45481400-45498400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr21:45481600-45486600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr21:45481600-45487600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr21:45481600-45489400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr21:45481600-45489600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr21:45481600-45502400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr21:45481600-45510800	Strong transcription	Dnd41	blood
35	chr21:45481600-45523800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr21:45481800-45487400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr21:45481800-45487400	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr21:45481800-45487600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr21:45481800-45487600	Strong transcription	Rectal Smooth Muscle	rectum
40	chr21:45481800-45487800	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr21:45481800-45488000	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr21:45481800-45489600	Strong transcription	Colonic Mucosa	Colon
43	chr21:45481800-45489800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr21:45481800-45490400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr21:45481800-45502600	Strong transcription	Left Ventricle	heart
46	chr21:45481800-45503800	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr21:45482000-45503000	Strong transcription	Primary B cells from cord blood	blood
48	chr21:45482200-45486400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr21:45482200-45486600	Strong transcription	Adipose Nuclei	Adipose
50	chr21:45482200-45487600	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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