Variant report

Variant	rs1468279
Chromosome Location	chr14:68925093-68925094
allele	A/C
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:32)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:32 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:68714111..68716167-chr14:68924259..68925879,2	MCF-7	breast:
2	chr14:68604795..68607491-chr14:68924394..68928105,4	MCF-7	breast:
3	chr14:68829901..68834300-chr14:68923345..68927378,4	MCF-7	breast:
4	chr14:68923972..68925932-chr14:69141412..69143252,2	MCF-7	breast:
5	chr14:68697755..68699525-chr14:68925028..68926847,2	MCF-7	breast:
6	chr14:68924227..68926055-chr14:69043237..69046222,3	MCF-7	breast:
7	chr14:68916802..68919938-chr14:68924497..68927794,5	MCF-7	breast:
8	chr14:68870904..68872882-chr14:68924657..68927546,2	MCF-7	breast:
9	chr14:68843357..68844886-chr14:68924790..68926556,2	MCF-7	breast:
10	chr14:68924906..68927378-chr14:69044527..69046149,2	MCF-7	breast:
11	chr14:68718829..68724499-chr14:68924135..68928480,8	MCF-7	breast:
12	chr14:68863962..68866276-chr14:68924626..68928147,6	MCF-7	breast:
13	chr14:68715136..68717167-chr14:68924205..68927016,2	MCF-7	breast:
14	chr14:68914909..68916568-chr14:68924870..68926386,2	MCF-7	breast:
15	chr14:68865212..68868859-chr14:68924955..68927209,3	MCF-7	breast:
16	chr14:68924273..68927929-chr14:69034368..69037492,4	MCF-7	breast:
17	chr14:68923760..68926395-chr14:69020012..69022778,2	MCF-7	breast:
18	chr14:68656976..68658957-chr14:68924252..68926500,2	MCF-7	breast:
19	chr14:68843051..68845983-chr14:68924155..68927430,4	MCF-7	breast:
20	chr14:68644184..68646511-chr14:68924637..68927356,2	MCF-7	breast:
21	chr14:68711454..68713449-chr14:68924641..68927109,2	MCF-7	breast:
22	chr14:68860545..68863012-chr14:68924709..68926828,2	MCF-7	breast:
23	chr14:68924822..68938526-chr14:69257377..69265713,29	MCF-7	breast:
24	chr14:68924131..68926741-chr17:57919265..57922255,2	MCF-7	breast:
25	chr14:68775050..68777034-chr14:68923914..68926374,3	MCF-7	breast:
26	chr14:68925011..68926542-chr14:69036351..69037638,115	MCF-7	breast:
27	chr14:68694692..68697256-chr14:68924013..68926249,2	MCF-7	breast:
28	chr14:68771578..68778202-chr14:68921843..68928978,14	MCF-7	breast:
29	chr14:68917247..68930048-chr14:69249444..69264210,56	MCF-7	breast:
30	chr14:68722033..68724723-chr14:68923948..68925904,2	MCF-7	breast:
31	chr14:68924187..68928322-chr14:68988163..68990816,4	MCF-7	breast:
32	chr14:68605361..68607383-chr14:68924952..68927307,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10130683	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10133813	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10135247	0.82[JPT][hapmap]
rs10136055	0.82[JPT][hapmap]
rs10138140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10139107	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10146058	0.85[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10146772	0.88[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap]
rs10148720	0.84[ASN][1000 genomes]
rs10149340	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10149349	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10467820	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10782456	0.82[ASN][1000 genomes]
rs12435914	0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs12587397	0.89[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12886429	0.87[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12886864	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1956534	0.96[GIH][hapmap];0.81[MEX][hapmap]
rs2040783	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2074562	0.84[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2074563	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074564	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074565	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2093202	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2097800	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2107340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2331701	0.96[CEU][hapmap]
rs2717217	0.82[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2842322	0.80[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs3784122	0.82[JPT][hapmap]
rs3784123	0.82[JPT][hapmap]
rs3784124	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4411448	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902594	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4902595	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4902596	0.83[ASN][1000 genomes]
rs5004090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61986936	0.83[ASN][1000 genomes]
rs6573837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs746663	0.96[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap]
rs8012610	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs9323508	0.83[ASW][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap]
rs9323512	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[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
rs1468279	MAP3K9	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68915600-68925400	Weak transcription	Colonic Mucosa	Colon
2	chr14:68916800-68925600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:68918600-68925600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr14:68918800-68925600	Weak transcription	Left Ventricle	heart
5	chr14:68921600-68925400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr14:68921800-68925600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr14:68921800-68925600	Weak transcription	Psoas Muscle	Psoas
8	chr14:68921800-68925800	Weak transcription	Aorta	Aorta
9	chr14:68922000-68925600	Weak transcription	Brain Substantia Nigra	brain
10	chr14:68922000-68925600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr14:68922000-68925600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr14:68922000-68925800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr14:68922200-68937600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr14:68924000-68925400	Weak transcription	Liver	Liver
15	chr14:68924000-68925600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr14:68924000-68925600	Enhancers	HUVEC	blood vessel
17	chr14:68924600-68926800	Enhancers	HepG2	liver
18	chr14:68924600-68926800	Enhancers	NHEK	skin
19	chr14:68924600-68931200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr14:68924800-68925600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr14:68924800-68925600	Enhancers	Rectal Smooth Muscle	rectum
22	chr14:68924800-68925600	Flanking Active TSS	A549	lung
23	chr14:68924800-68925600	Enhancers	Hela-S3	cervix
24	chr14:68924800-68925600	Enhancers	NH-A	brain
25	chr14:68924800-68926400	Enhancers	Fetal Kidney	kidney
26	chr14:68924800-68926600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr14:68924800-68926600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr14:68924800-68926800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr14:68924800-68926800	Enhancers	HMEC	breast
30	chr14:68924800-68927000	Enhancers	Fetal Lung	lung
31	chr14:68924800-68927000	Enhancers	Small Intestine	intestine
32	chr14:68924800-68927400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr14:68924800-68928800	Enhancers	Fetal Muscle Leg	muscle
34	chr14:68924800-68929800	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr14:68924800-68936000	Enhancers	HSMM	muscle
36	chr14:68925000-68925400	Weak transcription	Colon Smooth Muscle	Colon
37	chr14:68925000-68925600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr14:68925000-68925800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr14:68925000-68926600	Enhancers	Duodenum Mucosa	Duodenum
40	chr14:68925000-68935200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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