Variant report

Variant	rs11101285
Chromosome Location	chr10:49497432-49497433
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr10:49497290-49498112	GM12878	blood:	n/a	chr10:49497431-49497443
2	SMC3	chr10:49497384-49498054	GM12878	blood:	n/a	chr10:49497881-49497889
3	CTCF	chr10:49497257-49498287	A549	lung:	n/a	n/a
4	RAD21	chr10:49497311-49498165	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr10:49497421-49498386	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:49423127..49424126-chr10:49497102..49498218,5	MCF-7	breast:
2	chr10:49494826..49497610-chr10:49513560..49515926,2	MCF-7	breast:
3	chr10:49496582..49501262-chr10:49513244..49517429,4	K562	blood:
4	chr10:49489462..49491590-chr10:49496144..49498930,2	MCF-7	breast:
5	chr10:49423144..49424160-chr10:49497116..49498379,10	MCF-7	breast:
6	chr10:49422440..49425186-chr10:49494550..49500073,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225482	TF binding region
ENSG00000107643	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10745265	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs10776592	1.00[JPT][hapmap]
rs10776594	1.00[JPT][hapmap]
rs10857564	1.00[JPT][hapmap]
rs10857565	1.00[JPT][hapmap]
rs1112268	1.00[JPT][hapmap]
rs11597435	1.00[JPT][hapmap]
rs11598320	0.93[JPT][hapmap]
rs12358297	1.00[JPT][hapmap]
rs17780725	1.00[JPT][hapmap]
rs1881735	1.00[JPT][hapmap]
rs1881737	1.00[JPT][hapmap]
rs1881740	1.00[JPT][hapmap]
rs1881741	1.00[JPT][hapmap]
rs1919706	1.00[JPT][hapmap]
rs1919707	0.93[JPT][hapmap]
rs1919709	1.00[JPT][hapmap]
rs1997365	0.87[CEU][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs2377143	0.94[JPT][hapmap]
rs2377349	1.00[JPT][hapmap]
rs2590386	1.00[JPT][hapmap]
rs2590391	1.00[JPT][hapmap]
rs2698758	1.00[JPT][hapmap]
rs2698768	1.00[JPT][hapmap]
rs2889595	1.00[JPT][hapmap]
rs4838404	0.81[GIH][hapmap];0.88[JPT][hapmap]
rs6537559	0.87[CEU][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs7068398	0.94[JPT][hapmap]
rs7097975	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs7898026	0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv550812	chr10:49484698-49524715	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11101285	PRAP1	trans	parietal	SCAN
rs11101285	MAPK8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49492400-49498200	Enhancers	Fetal Thymus	thymus
2	chr10:49493200-49499800	Enhancers	GM12878-XiMat	blood
3	chr10:49493600-49504200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:49494000-49497600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr10:49494400-49498000	Weak transcription	Adipose Nuclei	Adipose
6	chr10:49495000-49498000	Enhancers	Brain Hippocampus Middle	brain
7	chr10:49495200-49497800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr10:49495200-49498200	Enhancers	Brain Substantia Nigra	brain
9	chr10:49495400-49497800	Enhancers	Brain Cingulate Gyrus	brain
10	chr10:49495400-49498200	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr10:49495400-49498800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr10:49495400-49500400	Enhancers	Placenta	Placenta
13	chr10:49495600-49497800	Enhancers	Fetal Lung	lung
14	chr10:49495600-49498200	Enhancers	Brain Anterior Caudate	brain
15	chr10:49495600-49498800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr10:49495800-49497800	Enhancers	Fetal Muscle Trunk	muscle
17	chr10:49495800-49498200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr10:49495800-49500400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr10:49496200-49497600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr10:49496200-49497600	Weak transcription	Fetal Brain Male	brain
21	chr10:49496200-49497800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr10:49496200-49498000	Weak transcription	Fetal Muscle Leg	muscle
23	chr10:49496400-49497600	Weak transcription	Stomach Mucosa	stomach
24	chr10:49496400-49497800	Weak transcription	NHEK	skin
25	chr10:49496400-49498000	Weak transcription	Brain Germinal Matrix	brain
26	chr10:49496400-49498800	Weak transcription	Gastric	stomach
27	chr10:49496400-49514200	Weak transcription	Right Atrium	heart
28	chr10:49496600-49497600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr10:49496600-49497600	Weak transcription	Right Ventricle	heart
30	chr10:49496800-49497600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr10:49496800-49501800	Enhancers	Dnd41	blood
32	chr10:49497000-49498000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr10:49497000-49499800	Enhancers	HepG2	liver
34	chr10:49497200-49497600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr10:49497200-49498000	Weak transcription	Pancreas	Pancrea
36	chr10:49497200-49498200	Enhancers	Brain Angular Gyrus	brain
37	chr10:49497200-49498400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr10:49497200-49499200	Enhancers	Duodenum Mucosa	Duodenum
39	chr10:49497400-49497800	Enhancers	NH-A	brain
40	chr10:49497400-49498000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr10:49497400-49498000	Enhancers	Esophagus	oesophagus
42	chr10:49497400-49498200	Enhancers	Colon Smooth Muscle	Colon
43	chr10:49497400-49498600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr10:49497400-49499800	Enhancers	Fetal Intestine Large	intestine

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