Variant report

Variant	rs741949
Chromosome Location	chr21:46256897-46256898
allele	G/T
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46254339..46258988-chr21:46290950..46295113,5	MCF-7	breast:
2	chr21:46247527..46250917-chr21:46254935..46257168,7	K562	blood:
3	chr21:46219617..46224872-chr21:46254277..46260376,11	MCF-7	breast:
4	chr21:46220501..46225374-chr21:46254982..46260084,8	K562	blood:
5	chr21:46254444..46259889-chr21:46289030..46296551,8	MCF-7	breast:
6	chr21:46256640..46259099-chr21:46259319..46260934,2	MCF-7	breast:
7	chr21:46234514..46239857-chr21:46252461..46259659,16	MCF-7	breast:
8	chr21:46255059..46257410-chr21:46492878..46495780,2	K562	blood:
9	chr21:46256501..46258560-chr21:46321252..46323907,2	MCF-7	breast:
10	chr21:46235858..46241119-chr21:46254955..46260994,15	MCF-7	breast:
11	chr21:46247527..46251136-chr21:46253947..46257899,9	K562	blood:
12	chr21:46256405..46259532-chr21:46270974..46273137,3	K562	blood:
13	chr21:46253493..46258173-chr21:46289318..46293722,5	K562	blood:
14	chr21:46255862..46258104-chr21:46297344..46299707,2	K562	blood:
15	chr21:46256501..46259929-chr21:46346281..46348601,3	MCF-7	breast:
16	chr21:46219746..46220652-chr21:46256461..46257271,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000183255	Chromatin interaction
ENSG00000268856	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000184900	Chromatin interaction
ENSG00000236519	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000184787	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11088966	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11088968	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13047791	0.96[ASN][1000 genomes]
rs13051307	0.84[JPT][hapmap]
rs13051895	0.80[JPT][hapmap]
rs17004706	0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs235258	0.96[ASN][1000 genomes]
rs2838701	0.82[ASW][hapmap];0.91[LWK][hapmap];0.81[MKK][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs34276405	0.99[ASN][1000 genomes]
rs34753953	0.96[ASN][1000 genomes]
rs34846682	0.99[ASN][1000 genomes]
rs34949239	0.96[ASN][1000 genomes]
rs35719912	0.91[ASN][1000 genomes]
rs4818735	0.99[ASN][1000 genomes]
rs4818736	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4818737	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4818979	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73372549	0.82[AFR][1000 genomes]
rs8132841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8133302	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9637165	0.97[ASN][1000 genomes]
rs9808690	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs9808742	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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
5	nsv459298	chr21:46223847-46277968	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv587813	chr21:46223847-46277968	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv913963	chr21:46223847-46277968	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv913964	chr21:46223847-46298869	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv913962	chr21:46223847-46321172	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv913965	chr21:46223847-46321172	Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv1058550	chr21:46227163-46317934	Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv913966	chr21:46229393-46261390	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
13	nsv913967	chr21:46249752-46279505	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv913968	chr21:46249752-46301008	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
15	nsv1060233	chr21:46254075-46323401	Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
16	nsv1056513	chr21:46254075-46442759	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
17	esv3341452	chr21:46254949-46257697	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
18	esv3347676	chr21:46255124-46257347	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
19	esv3423340	chr21:46255574-46258372	Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs741949	KRTAP10-11	cis	cerebellum	SCAN
rs741949	KRTAP10-1	cis	parietal	SCAN
rs741949	PCBP3	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46255200-46257200	Enhancers	Right Ventricle	heart
2	chr21:46255200-46257600	Enhancers	Duodenum Mucosa	Duodenum
3	chr21:46255400-46257000	Enhancers	Fetal Muscle Trunk	muscle
4	chr21:46255400-46258800	Enhancers	Fetal Muscle Leg	muscle
5	chr21:46255600-46257000	Enhancers	Brain Anterior Caudate	brain
6	chr21:46255600-46257400	Enhancers	Placenta	Placenta
7	chr21:46256400-46257000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr21:46256400-46257000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr21:46256400-46257000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr21:46256400-46257000	Enhancers	Adipose Nuclei	Adipose
11	chr21:46256400-46257000	Enhancers	Brain Hippocampus Middle	brain
12	chr21:46256400-46257000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
13	chr21:46256400-46257000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr21:46256400-46257000	Enhancers	Brain Substantia Nigra	brain
15	chr21:46256400-46257000	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr21:46256400-46257000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
17	chr21:46256400-46257000	Enhancers	Fetal Intestine Large	intestine
18	chr21:46256400-46257000	Enhancers	Pancreas	Pancrea
19	chr21:46256400-46257000	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr21:46256400-46257000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
21	chr21:46256400-46257000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
22	chr21:46256400-46257000	Enhancers	Osteobl	bone
23	chr21:46256400-46257200	Enhancers	Fetal Intestine Small	intestine
24	chr21:46256400-46257200	Enhancers	Gastric	stomach
25	chr21:46256400-46257200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr21:46256400-46257200	Bivalent Enhancer	NHEK	skin
27	chr21:46256400-46257400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr21:46256400-46257400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
29	chr21:46256400-46257400	Bivalent Enhancer	Stomach Mucosa	stomach
30	chr21:46256400-46257600	Flanking Bivalent TSS/Enh	HepG2	liver
31	chr21:46256400-46257800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr21:46256400-46257800	Enhancers	H1 Cell Line	embryonic stem cell
33	chr21:46256400-46257800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr21:46256400-46258400	Enhancers	HSMMtube	muscle
35	chr21:46256400-46258800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr21:46256400-46259200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr21:46256600-46257000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr21:46256600-46257000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr21:46256600-46257000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr21:46256600-46257000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr21:46256600-46257000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr21:46256600-46257000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr21:46256600-46257000	Enhancers	Brain Cingulate Gyrus	brain
44	chr21:46256600-46257000	Enhancers	Colon Smooth Muscle	Colon
45	chr21:46256600-46257000	Enhancers	Esophagus	oesophagus
46	chr21:46256600-46257000	Enhancers	Left Ventricle	heart
47	chr21:46256600-46257000	Flanking Active TSS	Spleen	Spleen
48	chr21:46256600-46257000	Enhancers	NHDF-Ad	bronchial
49	chr21:46256600-46257200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr21:46256600-46257200	Enhancers	Cortex derived primary cultured neurospheres	brain

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