Variant report

Variant	rs10501375
Chromosome Location	chr11:58966176-58966177
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:58965350..58967511-chr11:58968556..58970578,2	K562	blood:
2	chr11:58965619..58966464-chr5:142419606..142420543,2	MCF-7	breast:
3	chr11:58960553..58962825-chr11:58964256..58966200,2	K562	blood:

Variant related genes	Relation type
ENSG00000110042	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1048696	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10501376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896949	0.82[EUR][1000 genomes]
rs10896950	0.82[EUR][1000 genomes]
rs10896957	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11229868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229870	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][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];1.00[ASN][1000 genomes]
rs11229872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229873	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229874	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229875	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229882	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11229889	0.84[ASW][hapmap];0.88[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs11229901	0.87[EUR][1000 genomes]
rs11229902	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs11229903	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs11229904	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12223401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12284370	0.82[EUR][1000 genomes]
rs12575770	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12576150	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12576412	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12576558	0.83[EUR][1000 genomes]
rs12576879	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12577252	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17153538	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1938595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35654554	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3740946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3781796	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59466005	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60028658	0.90[AFR][1000 genomes]
rs60265864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61086875	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7104296	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7104437	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7926933	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7942203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869155	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10501375	CCDC86	cis	parietal	SCAN
rs10501375	DTX4	cis	lymphoblastoid	seeQTL
rs10501375	DTX4	Cis_1M	lymphoblastoid	RTeQTL
rs10501375	MPEG1	cis	lymphoblastoid	seeQTL
rs10501375	WDR74	cis	parietal	SCAN
rs10501375	MPEG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58943600-58975400	Weak transcription	NHEK	skin
2	chr11:58949400-58973400	Weak transcription	Right Ventricle	heart
3	chr11:58950000-58978400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:58950400-58972200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr11:58954600-58966200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:58955000-58967200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr11:58955400-58970800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr11:58956400-58977400	Weak transcription	Hela-S3	cervix
9	chr11:58957000-58967600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:58958600-58968400	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:58959200-58967600	Strong transcription	Duodenum Mucosa	Duodenum
12	chr11:58959400-58968400	Strong transcription	Fetal Intestine Large	intestine
13	chr11:58959400-58968800	Weak transcription	HepG2	liver
14	chr11:58959600-58974600	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr11:58959800-58968400	Strong transcription	Fetal Intestine Small	intestine
16	chr11:58959800-58968400	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr11:58960400-58974800	Weak transcription	Aorta	Aorta
18	chr11:58962000-58967600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:58962200-58969400	Genic enhancers	Adipose Nuclei	Adipose
20	chr11:58962800-58975000	Genic enhancers	Primary B cells from peripheral blood	blood
21	chr11:58963000-58968800	Weak transcription	Esophagus	oesophagus
22	chr11:58963200-58968400	Weak transcription	Spleen	Spleen
23	chr11:58963200-58972200	Weak transcription	Small Intestine	intestine
24	chr11:58963400-58973800	Weak transcription	Primary T cells from cord blood	blood
25	chr11:58963600-58969000	Genic enhancers	Primary B cells from cord blood	blood
26	chr11:58964200-58968400	Weak transcription	Colonic Mucosa	Colon
27	chr11:58964200-58976000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:58964400-58967200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:58964400-58968200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr11:58964400-58977400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:58964600-58966800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:58964600-58967000	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr11:58964600-58968600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr11:58964600-58968800	Weak transcription	HMEC	breast
35	chr11:58964600-58969200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr11:58964600-58971800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr11:58964600-58972000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr11:58964800-58966200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr11:58964800-58966200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:58964800-58966800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr11:58964800-58967600	Genic enhancers	Fetal Stomach	stomach
42	chr11:58964800-58967800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr11:58964800-58968400	Weak transcription	Gastric	stomach
44	chr11:58964800-58968600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr11:58964800-58972200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr11:58964800-58975600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr11:58965000-58966200	Enhancers	Primary hematopoietic stem cells	blood
48	chr11:58965000-58966200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr11:58965000-58966400	Enhancers	Brain Hippocampus Middle	brain
50	chr11:58965000-58966400	Enhancers	Brain Substantia Nigra	brain

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