Variant report

Variant	rs2300875
Chromosome Location	chr14:69438984-69438985
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:69402982..69422523-chr14:69436263..69448017,46	MCF-7	breast:

Variant related genes	Relation type
ENSG00000072110	Chromatin interaction
ENSG00000258531	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1007407	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10083451	0.82[JPT][hapmap]
rs10130013	1.00[JPT][hapmap]
rs10137547	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10139873	0.82[JPT][hapmap]
rs10143302	1.00[JPT][hapmap]
rs10145565	0.82[JPT][hapmap]
rs10146339	1.00[JPT][hapmap]
rs10147369	1.00[JPT][hapmap]
rs10147976	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10149232	1.00[JPT][hapmap]
rs11158782	0.82[JPT][hapmap]
rs11158787	1.00[JPT][hapmap]
rs11158790	0.82[JPT][hapmap]
rs1147481	0.82[JPT][hapmap]
rs11620922	0.96[EUR][1000 genomes]
rs11622889	1.00[JPT][hapmap]
rs11628126	1.00[JPT][hapmap]
rs12431846	1.00[JPT][hapmap]
rs12432970	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs12434478	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs12434775	1.00[JPT][hapmap]
rs12435594	1.00[JPT][hapmap]
rs12589028	0.82[JPT][hapmap]
rs1275407	0.82[JPT][hapmap]
rs1275415	1.00[JPT][hapmap]
rs17093668	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs17106670	0.90[ASN][1000 genomes]
rs1892297	1.00[JPT][hapmap]
rs1914004	1.00[JPT][hapmap]
rs2001998	0.82[JPT][hapmap]
rs2012750	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2012764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2012785	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024892	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2024893	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs2056153	1.00[JPT][hapmap]
rs2268968	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs28561965	1.00[ASN][1000 genomes]
rs28613298	0.82[JPT][hapmap]
rs3809393	0.95[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs4243632	0.96[ASN][1000 genomes]
rs4902682	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs6573869	0.82[JPT][hapmap]
rs7140693	0.88[CHD][hapmap]
rs7149487	0.90[ASN][1000 genomes]
rs7160629	0.82[JPT][hapmap]
rs72733548	0.86[ASN][1000 genomes]
rs8008184	1.00[JPT][hapmap]
rs8016537	0.87[ASN][1000 genomes]
rs9323524	0.82[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832823	chr14:69388853-69567638	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2300875	ACTN1	Cis_1M	lymphoblastoid	RTeQTL
rs2300875	FNTB	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69411200-69442600	Weak transcription	Fetal Brain Female	brain
2	chr14:69420200-69441200	Genic enhancers	NHEK	skin
3	chr14:69420600-69441600	Genic enhancers	NH-A	brain
4	chr14:69421200-69442200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr14:69428400-69442200	Genic enhancers	Fetal Stomach	stomach
6	chr14:69428600-69439800	Genic enhancers	Fetal Intestine Small	intestine
7	chr14:69428600-69443400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr14:69429200-69439600	Enhancers	Fetal Thymus	thymus
9	chr14:69429400-69443800	Weak transcription	Brain Germinal Matrix	brain
10	chr14:69429800-69441400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr14:69429800-69442400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr14:69430000-69440400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:69430000-69441600	Genic enhancers	HSMM	muscle
14	chr14:69430800-69439000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr14:69431800-69439200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr14:69431800-69444000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
17	chr14:69432000-69442400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr14:69432400-69441400	Genic enhancers	HepG2	liver
19	chr14:69432600-69442200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr14:69432600-69443000	Weak transcription	Brain Substantia Nigra	brain
21	chr14:69433200-69442000	Genic enhancers	Muscle Satellite Cultured Cells	--
22	chr14:69434200-69441600	Weak transcription	Ovary	ovary
23	chr14:69434400-69442400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr14:69434600-69440400	Weak transcription	K562	blood
25	chr14:69434800-69439200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr14:69435200-69439400	Enhancers	Primary T cells fromperipheralblood	blood
27	chr14:69435600-69439200	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr14:69435600-69441600	Genic enhancers	HMEC	breast
29	chr14:69436000-69439200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr14:69436200-69442600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr14:69436400-69441800	Weak transcription	Brain Angular Gyrus	brain
32	chr14:69436600-69439000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr14:69436600-69442000	Weak transcription	Brain Hippocampus Middle	brain
34	chr14:69437000-69439200	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr14:69437000-69439400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr14:69437000-69439400	Weak transcription	Placenta	Placenta
37	chr14:69437000-69443000	Weak transcription	Fetal Brain Male	brain
38	chr14:69437200-69439200	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr14:69437200-69439400	Weak transcription	Adipose Nuclei	Adipose
40	chr14:69437200-69441400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr14:69437200-69442000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr14:69437400-69439000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr14:69437400-69439000	Enhancers	Thymus	Thymus
44	chr14:69437400-69439600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr14:69437400-69440600	Weak transcription	Right Ventricle	heart
46	chr14:69437400-69441400	Weak transcription	Small Intestine	intestine
47	chr14:69437400-69441800	Genic enhancers	A549	lung
48	chr14:69437400-69441800	Genic enhancers	Osteobl	bone
49	chr14:69437400-69442200	Genic enhancers	HUVEC	blood vessel
50	chr14:69437600-69439400	Enhancers	Primary T helper cells PMA-I stimulated	--

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