Variant report

Variant	rs2316901
Chromosome Location	chr11:8679016-8679017
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8673819..8675893-chr11:8677657..8679340,2	MCF-7	breast:
2	chr11:8676736..8679603-chr11:8698205..8700155,2	K562	blood:
3	chr11:8674907..8677648-chr11:8677971..8679721,2	K562	blood:
4	chr11:8668653..8671494-chr11:8678160..8679778,3	K562	blood:

Variant related genes	Relation type
ENSG00000166436	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10128597	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10769908	0.84[MEX][hapmap]
rs10769931	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10769932	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10769936	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10769938	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10769939	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10840100	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10840102	0.99[ASN][1000 genomes]
rs10840104	0.99[ASN][1000 genomes]
rs11041978	0.84[MEX][hapmap]
rs11042016	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11042017	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11042018	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11042023	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11042025	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11042029	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11042030	0.99[ASN][1000 genomes]
rs12271470	0.99[ASN][1000 genomes]
rs12575252	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12803166	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1502317	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2028882	0.84[MEX][hapmap]
rs34867877	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35319120	0.97[ASN][1000 genomes]
rs36092927	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4256980	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4272783	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4291677	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4495896	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4503528	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4929923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4929924	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4929925	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4929926	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4929927	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4929928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4929942	0.83[MEX][hapmap]
rs4929943	0.84[MEX][hapmap]
rs4929947	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4929948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6486253	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7110529	0.94[ASN][1000 genomes]
rs7113874	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7118611	0.99[ASN][1000 genomes]
rs7126235	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs725502	0.84[MEX][hapmap]
rs7939673	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7939731	0.84[MEX][hapmap]
rs7941510	0.99[ASN][1000 genomes]
rs7945659	0.91[MEX][hapmap]
rs7950166	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7950528	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs885114	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9300092	0.84[MEX][hapmap]
rs9736791	0.84[MEX][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	esv2751035	chr11:8431654-8685451	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv896983	chr11:8526643-8682465	ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2316901	CNGA4	cis	cerebellum	SCAN
rs2316901	RPL27A	cis	parietal	SCAN
rs2316901	OR51V1	cis	cerebellum	SCAN
rs2316901	ST5	cis	cerebellum	SCAN
rs2316901	OR10A4	cis	parietal	SCAN
rs2316901	OR52E2	cis	parietal	SCAN
rs2316901	SNORA45	cis	cerebellum	SCAN
rs2316901	PKD1L2	trans	cerebellum	SCAN
rs2316901	RPL27A	cis	cerebellum	SCAN
rs2316901	OR56B4	cis	parietal	SCAN
rs2316901	IPO7	cis	cerebellum	SCAN
rs2316901	SNORA45	cis	parietal	SCAN
rs2316901	STK33	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8637000-8703200	Weak transcription	Small Intestine	intestine
2	chr11:8662600-8680200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:8662600-8692000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr11:8663000-8680200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr11:8663200-8680000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:8663800-8679800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:8664200-8692800	Weak transcription	K562	blood
8	chr11:8664200-8700400	Weak transcription	Stomach Mucosa	stomach
9	chr11:8664400-8679600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr11:8664800-8679200	Weak transcription	Fetal Brain Male	brain
11	chr11:8664800-8679800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:8665800-8692600	Weak transcription	Fetal Kidney	kidney
13	chr11:8668200-8692400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr11:8668400-8692400	Weak transcription	A549	lung
15	chr11:8669200-8683200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr11:8669400-8693000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr11:8669600-8679800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr11:8669800-8691800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr11:8670000-8693400	Weak transcription	Colonic Mucosa	Colon
20	chr11:8670000-8693600	Weak transcription	Psoas Muscle	Psoas
21	chr11:8670200-8679600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:8670200-8679800	Weak transcription	Fetal Lung	lung
23	chr11:8670200-8692400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr11:8670200-8692800	Weak transcription	Left Ventricle	heart
25	chr11:8670200-8692800	Weak transcription	Ovary	ovary
26	chr11:8670200-8693200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr11:8670400-8680000	Weak transcription	Brain Hippocampus Middle	brain
28	chr11:8670400-8690400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:8670400-8693200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr11:8670600-8679400	Weak transcription	Fetal Muscle Leg	muscle
31	chr11:8670600-8686400	Weak transcription	HepG2	liver
32	chr11:8670600-8692800	Weak transcription	Primary B cells from cord blood	blood
33	chr11:8671200-8691200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr11:8671200-8693200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr11:8671400-8680000	Weak transcription	Brain Substantia Nigra	brain
36	chr11:8671400-8684400	Weak transcription	Fetal Intestine Large	intestine
37	chr11:8671400-8692400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr11:8671600-8679400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr11:8671600-8679600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr11:8671600-8684400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr11:8671600-8690400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:8671600-8690400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:8671600-8692400	Weak transcription	Fetal Thymus	thymus
44	chr11:8671600-8692600	Weak transcription	Fetal Stomach	stomach
45	chr11:8671600-8692600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr11:8671600-8692600	Weak transcription	Hela-S3	cervix
47	chr11:8671600-8692800	Weak transcription	Lung	lung
48	chr11:8671600-8693200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr11:8671600-8693400	Weak transcription	Gastric	stomach
50	chr11:8671800-8679800	Weak transcription	Brain Inferior Temporal Lobe	brain

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