Variant report

Variant	rs11827818
Chromosome Location	chr11:120198728-120198729
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:120105904..120108316-chr11:120197614..120199213,2	K562	blood:
2	chr11:120196351..120198435-chr11:120198442..120200347,2	MCF-7	breast:
3	chr11:120174600..120176592-chr11:120196059..120198854,2	K562	blood:

Variant related genes	Relation type
ENSG00000181264	Chromatin interaction
ENSG00000137709	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10502235	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10750173	0.84[JPT][hapmap]
rs10790381	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10790383	0.84[JPT][hapmap]
rs10892563	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs10892565	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10892566	0.84[JPT][hapmap]
rs10892569	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10892575	0.84[EUR][1000 genomes]
rs11217821	0.84[JPT][hapmap]
rs11217843	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11217857	0.86[EUR][1000 genomes]
rs11217874	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11217875	0.81[ASW][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs11601535	0.82[JPT][hapmap]
rs11823264	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11823300	0.95[ASN][1000 genomes]
rs11824032	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12270397	0.89[EUR][1000 genomes]
rs12361632	0.97[ASN][1000 genomes]
rs12785387	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12794618	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12806740	0.84[JPT][hapmap]
rs12807097	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17123861	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1812974	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1892894	0.84[JPT][hapmap]
rs1893261	0.84[JPT][hapmap]
rs2276035	1.00[ASW][hapmap];0.88[CEU][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap]
rs2305008	0.84[JPT][hapmap]
rs2305010	0.84[JPT][hapmap]
rs4381380	0.94[JPT][hapmap]
rs4936517	0.88[ASN][1000 genomes]
rs4938799	0.84[JPT][hapmap]
rs4938802	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4938803	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4938804	0.84[JPT][hapmap]
rs4938805	0.84[JPT][hapmap]
rs4938807	0.81[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs4938808	0.84[JPT][hapmap]
rs6589812	0.84[JPT][hapmap]
rs7121779	0.84[JPT][hapmap]
rs7129944	1.00[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs7131597	0.84[JPT][hapmap]
rs723937	0.84[JPT][hapmap]
rs7933086	0.84[JPT][hapmap]
rs7939137	0.84[JPT][hapmap]
rs7948928	0.84[JPT][hapmap]
rs894839	0.84[JPT][hapmap]

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	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11827818	TMEM136	cis	parietal	SCAN
rs11827818	SIDT2	cis	parietal	SCAN
rs11827818	ARHGEF12	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120196400-120206400	Weak transcription	Gastric	stomach
2	chr11:120196600-120200600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:120196600-120200800	Weak transcription	Esophagus	oesophagus
4	chr11:120196800-120198800	Enhancers	Fetal Intestine Large	intestine
5	chr11:120196800-120200600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:120196800-120205800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:120196800-120205800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:120196800-120206200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:120197000-120199200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:120197000-120199200	Weak transcription	Spleen	Spleen
11	chr11:120197000-120199400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:120197000-120200600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr11:120197000-120200800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:120197000-120201800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr11:120197200-120199200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr11:120197200-120199200	Weak transcription	Fetal Kidney	kidney
17	chr11:120197200-120199400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr11:120197200-120199600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr11:120197200-120200600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr11:120197200-120200600	Weak transcription	Adipose Nuclei	Adipose
21	chr11:120197200-120200600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr11:120197200-120200600	Weak transcription	Fetal Stomach	stomach
23	chr11:120197200-120200600	Weak transcription	Left Ventricle	heart
24	chr11:120197200-120200800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr11:120197200-120201000	Weak transcription	HMEC	breast
26	chr11:120197200-120205800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:120197200-120205800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr11:120197400-120198800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:120197400-120199200	Enhancers	NHDF-Ad	bronchial
30	chr11:120197400-120200600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:120197400-120200600	Enhancers	Fetal Heart	heart
32	chr11:120197400-120200600	Weak transcription	NHEK	skin
33	chr11:120197400-120200800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr11:120197600-120200600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr11:120197600-120200600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr11:120197600-120205800	Weak transcription	Liver	Liver
37	chr11:120197800-120199200	Weak transcription	Colon Smooth Muscle	Colon
38	chr11:120197800-120199400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr11:120197800-120199600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:120197800-120199800	Weak transcription	HUVEC	blood vessel
41	chr11:120197800-120200400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:120197800-120200600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr11:120197800-120200600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr11:120197800-120200600	Weak transcription	Aorta	Aorta
45	chr11:120197800-120200600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr11:120197800-120205600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr11:120198000-120199200	Weak transcription	K562	blood
48	chr11:120198000-120199400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:120198000-120199400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:120198000-120200600	Weak transcription	Fetal Muscle Leg	muscle

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