Variant report

Variant	rs10146058
Chromosome Location	chr14:68941237-68941238
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:68774341..68775925-chr14:68938870..68941254,2	MCF-7	breast:
2	chr14:68939895..68941707-chr14:68980300..68982996,2	MCF-7	breast:
3	chr14:68930492..68947840-chr14:69251918..69264148,62	MCF-7	breast:
4	chr14:68941174..68942779-chr14:68948287..68949886,2	MCF-7	breast:
5	chr14:68939074..68942142-chr14:68974708..68977098,3	MCF-7	breast:
6	chr14:68939193..68941696-chr14:68948813..68950407,2	K562	blood:
7	chr14:68931847..68934865-chr14:68939017..68942648,4	MCF-7	breast:
8	chr14:68941036..68943975-chr14:68946841..68948622,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10130683	0.83[ASN][1000 genomes]
rs10132294	0.95[GIH][hapmap];0.81[JPT][hapmap]
rs10133813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10135247	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs10136055	0.94[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.81[ASN][1000 genomes]
rs10138140	0.85[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10139107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10142629	0.83[ASN][1000 genomes]
rs10146321	0.89[GIH][hapmap]
rs10148720	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10149340	0.82[ASN][1000 genomes]
rs10162434	0.81[JPT][hapmap]
rs10467820	0.85[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs10782456	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158743	0.94[GIH][hapmap]
rs12435914	0.82[JPT][hapmap]
rs12587397	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12717531	0.83[GIH][hapmap]
rs12886429	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12886864	0.85[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12889770	0.83[GIH][hapmap]
rs1468279	0.85[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2040783	0.83[ASN][1000 genomes]
rs2074562	0.82[JPT][hapmap]
rs2074563	0.85[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2074564	0.82[ASN][1000 genomes]
rs2074565	0.84[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2093202	0.82[ASN][1000 genomes]
rs2097800	0.85[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2107340	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2717217	0.82[JPT][hapmap]
rs2753404	0.81[JPT][hapmap]
rs2842318	0.87[ASN][1000 genomes]
rs2842322	0.82[JPT][hapmap]
rs3784122	0.94[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.81[ASN][1000 genomes]
rs3784123	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs3784124	0.82[ASN][1000 genomes]
rs4411448	0.84[ASN][1000 genomes]
rs4902590	0.81[ASN][1000 genomes]
rs4902591	0.81[ASN][1000 genomes]
rs4902592	0.83[ASN][1000 genomes]
rs4902595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902596	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5004090	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs6573837	0.91[JPT][hapmap];0.83[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	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv832822	chr14:68874640-69060272	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10146058	KIAA0247	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68927600-68943800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr14:68928600-68949000	Weak transcription	Thymus	Thymus
3	chr14:68932200-68950000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr14:68933000-68946600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr14:68933400-68943000	Weak transcription	Right Atrium	heart
6	chr14:68933400-68943400	Weak transcription	Left Ventricle	heart
7	chr14:68933600-68942800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr14:68933600-68950600	Weak transcription	Aorta	Aorta
9	chr14:68933800-68942600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr14:68934200-68946200	Enhancers	Primary B cells from peripheral blood	blood
11	chr14:68935400-68943400	Weak transcription	Fetal Thymus	thymus
12	chr14:68935800-68943200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr14:68935800-68943400	Weak transcription	Gastric	stomach
14	chr14:68936000-68942600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr14:68936000-68942800	Weak transcription	HSMM	muscle
16	chr14:68936000-68943600	Weak transcription	Brain Hippocampus Middle	brain
17	chr14:68936000-68943600	Weak transcription	Esophagus	oesophagus
18	chr14:68936000-68947600	Weak transcription	Primary T cells from cord blood	blood
19	chr14:68936200-68942800	Weak transcription	Hela-S3	cervix
20	chr14:68936200-68943600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr14:68936200-68943600	Weak transcription	Brain Anterior Caudate	brain
22	chr14:68936800-68943400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr14:68936800-68944800	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr14:68937400-68942800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr14:68937800-68941800	Weak transcription	Fetal Intestine Small	intestine
26	chr14:68937800-68942800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr14:68937800-68942800	Weak transcription	Osteobl	bone
28	chr14:68938600-68942600	Weak transcription	Adipose Nuclei	Adipose
29	chr14:68938800-68941800	Weak transcription	HepG2	liver
30	chr14:68938800-68942800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr14:68938800-68944200	Enhancers	Liver	Liver
32	chr14:68939000-68943400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr14:68939000-68947400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr14:68939000-68951600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr14:68939200-68943400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr14:68939200-68943400	Weak transcription	Lung	lung
37	chr14:68939600-68943600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr14:68939800-68942800	Weak transcription	Stomach Mucosa	stomach
39	chr14:68940000-68943400	Weak transcription	Colon Smooth Muscle	Colon
40	chr14:68940200-68941400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr14:68940200-68941600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr14:68940200-68941600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr14:68940200-68941800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr14:68940200-68942000	Weak transcription	Primary B cells from cord blood	blood
45	chr14:68940200-68942200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr14:68940200-68942400	Weak transcription	GM12878-XiMat	blood
47	chr14:68940200-68942600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr14:68940200-68942600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr14:68940200-68942600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr14:68940200-68942800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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