Variant report

Variant	rs2838677
Chromosome Location	chr21:46189767-46189768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45896417..45898596-chr21:46188408..46190789,2	MCF-7	breast:
2	chr21:46188637..46191346-chr21:46209977..46212870,2	MCF-7	breast:
3	chr21:46182776..46184894-chr21:46189262..46192289,3	K562	blood:
4	chr21:46187475..46189831-chr21:46347988..46350104,2	MCF-7	breast:
5	chr21:46185632..46187378-chr21:46187744..46189857,2	K562	blood:
6	chr21:46188583..46191160-chr21:46207285..46209699,2	K562	blood:

Variant related genes	Relation type
ENSG00000273027	Chromatin interaction
ENSG00000160255	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs13047692	0.94[ASN][1000 genomes]
rs13047718	0.94[ASN][1000 genomes]
rs13051119	0.80[ASN][1000 genomes]
rs13433413	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2294158	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838679	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2838681	0.81[LWK][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs2838683	0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs2838693	0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs2838697	0.91[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs2838698	0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs2838700	0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs34875321	0.92[ASN][1000 genomes]
rs3788138	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4818731	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4818976	0.97[ASN][1000 genomes]
rs4818977	0.94[ASN][1000 genomes]
rs72613649	0.92[ASN][1000 genomes]
rs8131444	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8132011	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9306115	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9306116	0.85[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs9637189	0.94[ASN][1000 genomes]
rs9977465	0.93[ASN][1000 genomes]
rs9977676	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9978131	0.81[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9981344	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap]
rs9984290	0.89[YRI][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	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2838677	KRTAP10-12	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46183600-46190800	Weak transcription	A549	lung
2	chr21:46185600-46190800	Weak transcription	Brain Anterior Caudate	brain
3	chr21:46185600-46190800	Weak transcription	Hela-S3	cervix
4	chr21:46185800-46192600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr21:46185800-46199600	Weak transcription	Stomach Mucosa	stomach
6	chr21:46186000-46189800	Weak transcription	HSMMtube	muscle
7	chr21:46186000-46190600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr21:46186000-46190800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr21:46186200-46189800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr21:46186200-46190800	Weak transcription	Osteobl	bone
11	chr21:46186200-46199400	Weak transcription	Right Atrium	heart
12	chr21:46186400-46189800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr21:46186400-46189800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr21:46186400-46190600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr21:46186400-46191000	Weak transcription	K562	blood
16	chr21:46186600-46189800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr21:46186600-46190000	Weak transcription	GM12878-XiMat	blood
18	chr21:46186600-46190800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr21:46186600-46190800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr21:46187000-46191000	Weak transcription	Brain Angular Gyrus	brain
21	chr21:46187000-46193000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr21:46187000-46193200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr21:46187000-46195400	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr21:46187000-46213000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr21:46187200-46190800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr21:46187200-46194600	Weak transcription	NHDF-Ad	bronchial
27	chr21:46187200-46197800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr21:46187600-46196200	Strong transcription	Thymus	Thymus
29	chr21:46187800-46196600	Strong transcription	Right Ventricle	heart
30	chr21:46187800-46199000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr21:46187800-46206200	Strong transcription	Fetal Thymus	thymus
32	chr21:46188000-46193000	Strong transcription	Fetal Intestine Small	intestine
33	chr21:46188000-46193400	Strong transcription	Lung	lung
34	chr21:46188000-46195800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr21:46188000-46196800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr21:46188000-46198600	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr21:46188000-46198600	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr21:46188000-46198800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr21:46188000-46199000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr21:46188000-46201600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr21:46188000-46203000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr21:46188000-46203200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr21:46188000-46208000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr21:46188200-46189800	Weak transcription	Primary B cells from cord blood	blood
45	chr21:46188200-46193400	Strong transcription	Placenta	Placenta
46	chr21:46188200-46195000	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr21:46188200-46197000	Strong transcription	Fetal Brain Female	brain
48	chr21:46188200-46197200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr21:46188200-46197200	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr21:46188200-46197400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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