Variant report

Variant	rs11858468
Chromosome Location	chr15:83693276-83693277
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	POLR2A	chr15:83692828-83693429	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:83692989-83693402	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:83678350..83680791-chr15:83692946..83695679,3	MCF-7	breast:
2	chr15:83680193..83681715-chr15:83693273..83695238,2	MCF-7	breast:
3	chr15:83684576..83687517-chr15:83693136..83695627,2	K562	blood:
4	chr15:83680931..83684060-chr15:83687587..83694949,8	K562	blood:

Variant related genes	Relation type
ENSG00000259767	TF binding region
ENSG00000260608	Chromatin interaction
ENSG00000169609	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs1010820	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs10152762	1.00[ASN][1000 genomes]
rs1045742	0.94[CEU][hapmap]
rs10520576	0.94[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs1075619	0.94[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1112404	0.94[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs11259965	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs11259968	0.83[EUR][1000 genomes]
rs11259969	0.94[CEU][hapmap]
rs11259970	0.83[EUR][1000 genomes]
rs11852408	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs11852446	0.83[EUR][1000 genomes]
rs11852496	0.94[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs11853498	0.94[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854888	0.82[EUR][1000 genomes]
rs11855639	0.82[EUR][1000 genomes]
rs11855722	1.00[ASN][1000 genomes]
rs11856164	0.94[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856806	0.83[EUR][1000 genomes]
rs11857428	0.85[EUR][1000 genomes]
rs11857641	1.00[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs11857990	0.89[GIH][hapmap]
rs11858162	1.00[CEU][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858377	0.94[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs12437558	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437858	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12437901	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438398	0.82[EUR][1000 genomes]
rs12438575	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439903	0.83[EUR][1000 genomes]
rs12440265	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440386	0.84[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs12440562	0.94[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441006	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441409	0.94[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441575	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441847	0.83[EUR][1000 genomes]
rs12441907	1.00[ASN][1000 genomes]
rs12442894	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs12443109	0.94[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs12443424	0.83[EUR][1000 genomes]
rs12591855	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs12593532	0.82[EUR][1000 genomes]
rs12593638	0.94[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs12595330	0.94[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs17359494	0.84[MEX][hapmap]
rs17361375	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17507693	0.84[EUR][1000 genomes]
rs17507763	0.84[EUR][1000 genomes]
rs17508610	0.94[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509233	0.94[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17567151	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs17567869	0.94[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs17568298	0.94[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17568459	0.94[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs2034618	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs41326445	0.94[CEU][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap]
rs4300612	1.00[ASN][1000 genomes]
rs4408505	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4423388	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4547301	1.00[ASN][1000 genomes]
rs4563011	0.94[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4572349	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779064	1.00[ASN][1000 genomes]
rs55683536	0.83[EUR][1000 genomes]
rs55691648	1.00[ASN][1000 genomes]
rs55933526	1.00[ASN][1000 genomes]
rs55934845	1.00[ASN][1000 genomes]
rs56045305	0.82[EUR][1000 genomes]
rs56052029	0.82[EUR][1000 genomes]
rs56352317	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57219675	0.83[EUR][1000 genomes]
rs57729044	0.83[EUR][1000 genomes]
rs58006707	0.83[EUR][1000 genomes]
rs58281154	0.83[EUR][1000 genomes]
rs58396076	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59896565	0.83[EUR][1000 genomes]
rs60344060	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60819629	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61267530	0.81[EUR][1000 genomes]
rs62010162	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010164	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010165	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010166	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010170	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010172	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010173	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010174	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010175	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010177	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010208	1.00[ASN][1000 genomes]
rs62010212	0.84[EUR][1000 genomes]
rs62010214	0.82[EUR][1000 genomes]
rs62010215	0.83[EUR][1000 genomes]
rs62010220	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010247	1.00[ASN][1000 genomes]
rs62010248	0.83[EUR][1000 genomes]
rs62010252	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010254	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010255	0.83[EUR][1000 genomes]
rs62010258	0.83[EUR][1000 genomes]
rs62011702	1.00[ASN][1000 genomes]
rs62011742	0.85[EUR][1000 genomes]
rs62011744	0.88[EUR][1000 genomes]
rs62011869	0.85[EUR][1000 genomes]
rs6603042	0.89[GIH][hapmap];1.00[ASN][1000 genomes]
rs66619192	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66757932	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67022650	0.85[EUR][1000 genomes]
rs7164083	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7165114	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs7165978	0.94[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs716886	0.85[GIH][hapmap]
rs7172590	1.00[ASN][1000 genomes]
rs7177462	0.85[GIH][hapmap]
rs72755992	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495630	0.94[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495911	0.94[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs8027577	0.94[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs8031723	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038486	0.94[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs8043224	0.94[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs965263	0.94[CEU][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs965264	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs9707895	0.82[EUR][1000 genomes];1.00[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	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11858468	C15orf40	cis	parietal	SCAN
rs11858468	BTBD1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83681000-83700200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:83681000-83705000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:83681200-83693400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:83681200-83698200	Weak transcription	NHLF	lung
5	chr15:83681200-83710200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:83681400-83698000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:83681400-83698400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:83681600-83698200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr15:83681600-83698200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:83681600-83732000	Weak transcription	Stomach Mucosa	stomach
11	chr15:83682000-83708400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:83682200-83708600	Weak transcription	Fetal Heart	heart
13	chr15:83683000-83723000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr15:83683400-83726600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:83684600-83695200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:83685600-83693800	Strong transcription	Fetal Muscle Leg	muscle
17	chr15:83686600-83695800	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:83687000-83708200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:83687200-83697000	Strong transcription	Fetal Intestine Large	intestine
20	chr15:83687600-83698400	Weak transcription	Brain Substantia Nigra	brain
21	chr15:83687600-83701200	Weak transcription	Fetal Brain Female	brain
22	chr15:83687600-83709600	Weak transcription	Brain Angular Gyrus	brain
23	chr15:83687800-83694000	Strong transcription	Fetal Intestine Small	intestine
24	chr15:83688000-83698600	Weak transcription	NH-A	brain
25	chr15:83688800-83708800	Weak transcription	Fetal Brain Male	brain
26	chr15:83689200-83693400	Weak transcription	Lung	lung
27	chr15:83689200-83695000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr15:83689200-83695000	Weak transcription	Thymus	Thymus
29	chr15:83689200-83695600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr15:83689200-83695800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr15:83689200-83695800	Weak transcription	Pancreas	Pancrea
32	chr15:83689200-83696200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:83689200-83696200	Weak transcription	Gastric	stomach
34	chr15:83689200-83698200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr15:83689200-83698200	Weak transcription	Aorta	Aorta
36	chr15:83689200-83698200	Weak transcription	Esophagus	oesophagus
37	chr15:83689200-83698200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr15:83689200-83698200	Weak transcription	Small Intestine	intestine
39	chr15:83689200-83698200	Weak transcription	Spleen	Spleen
40	chr15:83689200-83698400	Weak transcription	Right Ventricle	heart
41	chr15:83689200-83705200	Weak transcription	Psoas Muscle	Psoas
42	chr15:83689400-83695800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr15:83689400-83696200	Weak transcription	Fetal Kidney	kidney
44	chr15:83689400-83696200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr15:83689400-83698200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr15:83689400-83698200	Weak transcription	Ovary	ovary
47	chr15:83689400-83705000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr15:83689400-83708600	Weak transcription	NHEK	skin
49	chr15:83689600-83696000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr15:83689600-83696200	Weak transcription	Adipose Nuclei	Adipose

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