Variant report

Variant	rs12886429
Chromosome Location	chr14:68948144-68948145
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:68946983..68949928-chr14:68952224..68954178,2	K562	blood:
2	chr14:68947089..68949808-chr14:68953310..68954848,2	MCF-7	breast:
3	chr14:68941036..68943975-chr14:68946841..68948622,2	MCF-7	breast:
4	chr14:68927281..68930277-chr14:68947615..68950464,3	MCF-7	breast:
5	chr14:68549698..68551582-chr14:68946778..68949306,2	MCF-7	breast:
6	chr14:68946730..68948878-chr14:68952615..68954751,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10130683	0.81[ASN][1000 genomes]
rs10132294	0.95[GIH][hapmap];0.81[JPT][hapmap]
rs10133813	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10135247	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10136055	0.94[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.81[ASN][1000 genomes]
rs10138140	0.87[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10139107	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10142629	0.81[ASN][1000 genomes]
rs10146058	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]
rs10146321	0.89[GIH][hapmap]
rs10148720	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10149340	0.81[ASN][1000 genomes]
rs10162434	0.81[JPT][hapmap]
rs10467820	0.87[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs10782456	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11158743	0.94[GIH][hapmap]
rs12435914	0.82[JPT][hapmap]
rs12587397	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12717531	0.83[GIH][hapmap]
rs12886864	0.87[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12889666	0.80[MEX][hapmap]
rs12889770	0.83[GIH][hapmap];0.80[MEX][hapmap]
rs1468279	0.87[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2040783	0.84[ASN][1000 genomes]
rs2074562	0.82[JPT][hapmap]
rs2074563	0.87[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2074564	0.82[ASN][1000 genomes]
rs2074565	0.86[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2093202	0.82[ASN][1000 genomes]
rs2097800	0.87[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2107340	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2717217	0.82[JPT][hapmap]
rs2753404	0.81[JPT][hapmap]
rs2842318	0.88[ASN][1000 genomes]
rs2842322	0.82[JPT][hapmap]
rs3784122	0.82[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.81[ASN][1000 genomes]
rs3784123	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs3784124	0.82[ASN][1000 genomes]
rs4411448	0.83[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];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902596	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5004090	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs6573837	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7160842	0.81[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
rs12886429	KIAA0247	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68928600-68949000	Weak transcription	Thymus	Thymus
2	chr14:68932200-68950000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr14:68933600-68950600	Weak transcription	Aorta	Aorta
4	chr14:68939000-68951600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr14:68940200-68949400	Weak transcription	Fetal Lung	lung
6	chr14:68943200-68949000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr14:68943400-68951600	Enhancers	Placenta	Placenta
8	chr14:68943600-68949600	Weak transcription	Fetal Kidney	kidney
9	chr14:68943800-68949000	Weak transcription	Colon Smooth Muscle	Colon
10	chr14:68943800-68950000	Weak transcription	Fetal Heart	heart
11	chr14:68943800-68957400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr14:68944000-68949200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr14:68944000-68950200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr14:68944000-68950400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr14:68944000-68959200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr14:68944200-68948800	Weak transcription	Stomach Mucosa	stomach
17	chr14:68944200-68949600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr14:68944200-68949600	Weak transcription	Fetal Thymus	thymus
19	chr14:68944200-68949800	Weak transcription	Spleen	Spleen
20	chr14:68944200-68950200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr14:68944200-68950200	Weak transcription	Gastric	stomach
22	chr14:68944200-68950800	Weak transcription	Osteobl	bone
23	chr14:68944200-68951800	Weak transcription	Liver	Liver
24	chr14:68944200-68953600	Weak transcription	Right Atrium	heart
25	chr14:68944200-68955000	Weak transcription	Esophagus	oesophagus
26	chr14:68944200-68957400	Weak transcription	Fetal Muscle Leg	muscle
27	chr14:68944400-68949600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr14:68944400-68949600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr14:68944400-68968200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr14:68944600-68948800	Weak transcription	Fetal Stomach	stomach
31	chr14:68944600-68949400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr14:68944600-68957400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr14:68944800-68949800	Weak transcription	NHDF-Ad	bronchial
34	chr14:68944800-68953800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr14:68945000-68951200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr14:68945200-68950000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr14:68945400-68949200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr14:68945400-68951800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr14:68945400-68959600	Weak transcription	Primary B cells from cord blood	blood
40	chr14:68945600-68950200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr14:68946000-68950200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr14:68946200-68949600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr14:68946200-68950200	Weak transcription	HUVEC	blood vessel
44	chr14:68946400-68948800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr14:68946400-68949400	Weak transcription	HMEC	breast
46	chr14:68946400-68949600	Weak transcription	K562	blood
47	chr14:68946400-68950200	Weak transcription	HepG2	liver
48	chr14:68946600-68949600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr14:68946600-68949600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr14:68946600-68949800	Weak transcription	NHEK	skin

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