Variant report

Variant	rs11204838
Chromosome Location	chr1:151493814-151493815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151491040..151494428-chr1:151495030..151499382,4	MCF-7	breast:
2	chr1:151426332..151429293-chr1:151493579..151495227,2	K562	blood:
3	chr1:151477348..151494376-chr1:151504804..151515249,50	MCF-7	breast:
4	chr1:151493742..151497338-chr1:151500122..151502548,3	MCF-7	breast:
5	chr1:151488223..151491246-chr1:151492945..151496772,3	K562	blood:
6	chr1:151429965..151433300-chr1:151491808..151494354,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143375	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000252840	Chromatin interaction
ENSG00000143442	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1009289	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10127622	0.89[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes]
rs10788807	0.87[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10788808	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10888418	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10888419	0.83[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11204827	0.91[JPT][hapmap]
rs11204828	0.91[JPT][hapmap]
rs11204834	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11204835	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11204837	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11204839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11583133	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12026585	0.81[ASN][1000 genomes]
rs12032983	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12118440	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12128578	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12730114	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1547832	0.83[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1573129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1573130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211435	0.83[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2298167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2337359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970955	0.91[JPT][hapmap]
rs61261719	0.82[ASN][1000 genomes]
rs6675984	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7548090	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7552458	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11204838	OTUD7B	cis	cerebellum	SCAN
rs11204838	TUFT1	cis	cerebellum	SCAN
rs11204838	LCE3E	cis	parietal	SCAN
rs11204838	SCNM1	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151484600-151512000	Weak transcription	Right Atrium	heart
2	chr1:151485200-151511800	Weak transcription	Fetal Brain Female	brain
3	chr1:151485800-151511800	Weak transcription	Brain Germinal Matrix	brain
4	chr1:151485800-151512200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:151486000-151501800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:151486600-151511800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:151486800-151512200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:151487000-151501800	Weak transcription	Esophagus	oesophagus
9	chr1:151487000-151511800	Weak transcription	Small Intestine	intestine
10	chr1:151487200-151502400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:151487400-151501000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:151489000-151497200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:151489000-151499400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:151489200-151507000	Weak transcription	NHEK	skin
15	chr1:151489200-151507400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:151490000-151496200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:151490800-151494000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:151490800-151494000	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr1:151491000-151494000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:151491000-151494000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:151491000-151494200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:151491000-151494600	Strong transcription	Fetal Stomach	stomach
23	chr1:151491000-151495000	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr1:151491000-151500000	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr1:151491000-151505200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr1:151491200-151494000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:151491600-151494000	Genic enhancers	Liver	Liver
28	chr1:151491600-151496600	Weak transcription	Lung	lung
29	chr1:151491600-151509000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:151491800-151494800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:151492000-151507400	Weak transcription	Stomach Mucosa	stomach
32	chr1:151492200-151496000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:151492600-151495800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:151492600-151496600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:151492800-151496600	Weak transcription	Brain Substantia Nigra	brain
36	chr1:151493000-151496600	Weak transcription	Brain Angular Gyrus	brain
37	chr1:151493000-151496800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:151493200-151494400	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:151493200-151495800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:151493200-151496000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:151493200-151496800	Weak transcription	GM12878-XiMat	blood
42	chr1:151493200-151497600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:151493200-151501000	Weak transcription	HMEC	breast
44	chr1:151493200-151507600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:151493400-151495600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:151493400-151495800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:151493400-151495800	Weak transcription	Gastric	stomach
48	chr1:151493400-151495800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:151493400-151495800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:151493400-151496000	Weak transcription	Brain Inferior Temporal Lobe	brain

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