Variant report

Variant	rs2074563
Chromosome Location	chr14:68935112-68935113
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:41)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr14:68935067-68936798	MCF-7	breast:	n/a	chr14:68935449-68935459 chr14:68936432-68936453
2	SIN3AK20	chr14:68935068-68936759	MCF-7	breast:	n/a	n/a
3	GATA2	chr14:68935032-68935851	HUVEC	blood vessel:	n/a	chr14:68935449-68935459
4	GABPA	chr14:68935088-68935838	MCF-7	breast:	n/a	n/a
5	CEBPB	chr14:68935084-68936465	MCF-7	breast:	n/a	n/a

No data

(count:41 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:68933809..68936461-chr14:69124608..69126436,2	MCF-7	breast:
2	chr14:68933801..68936110-chr14:68987785..68990032,2	MCF-7	breast:
3	chr14:68933689..68937829-chr14:68938571..68943232,4	K562	blood:
4	chr14:68714912..68718303-chr14:68931649..68935294,4	MCF-7	breast:
5	chr14:68868129..68871052-chr14:68933938..68936786,3	MCF-7	breast:
6	chr14:68934923..68936704-chr14:68952698..68955453,2	MCF-7	breast:
7	chr14:68932415..68937640-chr14:69040451..69046051,7	MCF-7	breast:
8	chr14:68744804..68746864-chr14:68934365..68937037,2	MCF-7	breast:
9	chr14:68925452..68926413-chr14:68935104..68936023,4	MCF-7	breast:
10	chr14:68884961..68886494-chr14:68933709..68935958,2	MCF-7	breast:
11	chr14:68931530..68935307-chr14:68935887..68938943,5	MCF-7	breast:
12	chr14:68858670..68861101-chr14:68933221..68935171,2	MCF-7	breast:
13	chr14:68877361..68878949-chr14:68933343..68936229,2	MCF-7	breast:
14	chr14:68862930..68865913-chr14:68933149..68936719,4	MCF-7	breast:
15	chr14:68410124..68413051-chr14:68932315..68935332,3	MCF-7	breast:
16	chr14:68932713..68936271-chr14:68973321..68975311,3	MCF-7	breast:
17	chr14:68934022..68936494-chr14:69279866..69281612,2	K562	blood:
18	chr14:68748170..68751386-chr14:68933626..68937180,4	MCF-7	breast:
19	chr14:68772153..68774683-chr14:68933663..68935450,3	MCF-7	breast:
20	chr14:68855816..68857966-chr14:68934020..68936825,3	MCF-7	breast:
21	chr14:68935034..68935823-chr14:69036590..69037270,2	MCF-7	breast:
22	chr14:68933425..68935782-chr14:68963190..68965749,2	MCF-7	breast:
23	chr14:68933643..68938139-chr14:68984805..68987652,4	MCF-7	breast:
24	chr14:68930492..68947840-chr14:69251918..69264148,62	MCF-7	breast:
25	chr14:68934261..68937173-chr14:68974215..68976515,2	MCF-7	breast:
26	chr14:68924822..68938526-chr14:69257377..69265713,29	MCF-7	breast:
27	chr14:68935023..68937975-chr14:68980944..68983030,2	MCF-7	breast:
28	chr14:68934627..68937001-chr14:69034855..69037345,2	MCF-7	breast:
29	chr14:68933089..68935511-chr14:69240196..69242436,2	MCF-7	breast:
30	chr14:68550172..68552587-chr14:68933806..68935725,2	MCF-7	breast:
31	chr14:68934148..68937192-chr14:68979856..68982063,3	MCF-7	breast:
32	chr14:68933594..68935776-chr14:68976787..68979201,2	MCF-7	breast:
33	chr14:68932825..68935217-chr14:69176276..69178496,2	MCF-7	breast:
34	chr14:68932040..68933583-chr14:68933760..68935630,2	MCF-7	breast:
35	chr14:68864311..68866713-chr14:68933323..68935955,2	MCF-7	breast:
36	chr14:68934455..68938409-chr14:69031168..69034448,4	MCF-7	breast:
37	chr14:68603270..68607294-chr14:68934008..68937330,4	MCF-7	breast:
38	chr14:68934889..68936879-chr14:68948786..68950483,2	MCF-7	breast:
39	chr14:68891874..68894078-chr14:68933895..68936431,2	MCF-7	breast:
40	chr14:68721992..68725773-chr14:68931800..68936275,3	MCF-7	breast:
41	chr14:68931687..68934408-chr14:68934726..68938256,5	MCF-7	breast:

No data

Variant related genes	Relation type
RAD51B	TF binding region
ENSG00000185650	Chromatin interaction
ENSG00000182185	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	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[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];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[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	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10149349	0.85[AMR][1000 genomes];0.87[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];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[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];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1468279	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]
rs1956534	0.96[GIH][hapmap];0.81[MEX][hapmap]
rs2040783	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2074562	0.84[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2074564	0.96[AMR][1000 genomes];1.00[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];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2093202	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[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];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[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];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4411448	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902594	0.89[AMR][1000 genomes];0.89[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];0.94[AMR][1000 genomes];0.99[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];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[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];0.92[AMR][1000 genomes];0.98[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
rs2074563	MAP3K9	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68922200-68937600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr14:68924800-68936000	Enhancers	HSMM	muscle
3	chr14:68925000-68935200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr14:68926000-68935200	Weak transcription	Gastric	stomach
5	chr14:68926200-68940000	Weak transcription	Ovary	ovary
6	chr14:68926600-68935600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr14:68926800-68937600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr14:68927000-68936600	Weak transcription	Primary B cells from cord blood	blood
9	chr14:68927600-68943800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr14:68928400-68939400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr14:68928600-68949000	Weak transcription	Thymus	Thymus
12	chr14:68929000-68937200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr14:68929400-68938000	Enhancers	HMEC	breast
14	chr14:68930600-68936200	Enhancers	HUVEC	blood vessel
15	chr14:68931200-68936200	Enhancers	NH-A	brain
16	chr14:68931600-68936200	Enhancers	Placenta	Placenta
17	chr14:68932200-68950000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr14:68932800-68938000	Enhancers	Placenta Amnion	Placenta Amnion
19	chr14:68933000-68936400	Enhancers	Stomach Mucosa	stomach
20	chr14:68933000-68946600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr14:68933200-68935400	Enhancers	Small Intestine	intestine
22	chr14:68933200-68936200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr14:68933200-68936400	Enhancers	Pancreas	Pancrea
24	chr14:68933400-68935200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr14:68933400-68935200	Weak transcription	Lung	lung
26	chr14:68933400-68935400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr14:68933400-68935400	Weak transcription	K562	blood
28	chr14:68933400-68936600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr14:68933400-68943000	Weak transcription	Right Atrium	heart
30	chr14:68933400-68943400	Weak transcription	Left Ventricle	heart
31	chr14:68933600-68935200	Weak transcription	Liver	Liver
32	chr14:68933600-68935200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr14:68933600-68935400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr14:68933600-68935600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr14:68933600-68935600	Weak transcription	Fetal Muscle Leg	muscle
36	chr14:68933600-68935600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr14:68933600-68936600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr14:68933600-68937200	Enhancers	NHEK	skin
39	chr14:68933600-68937400	Enhancers	A549	lung
40	chr14:68933600-68937600	Weak transcription	Psoas Muscle	Psoas
41	chr14:68933600-68938000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr14:68933600-68938000	Weak transcription	Adipose Nuclei	Adipose
43	chr14:68933600-68939800	Weak transcription	Fetal Stomach	stomach
44	chr14:68933600-68942800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr14:68933600-68950600	Weak transcription	Aorta	Aorta
46	chr14:68933800-68935200	Weak transcription	Fetal Lung	lung
47	chr14:68933800-68935200	Weak transcription	Hela-S3	cervix
48	chr14:68933800-68935400	Weak transcription	HSMMtube	muscle
49	chr14:68933800-68936800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr14:68933800-68937000	Weak transcription	Monocytes-CD14+_RO01746	blood

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