Variant report

Variant	rs913590
Chromosome Location	chr9:7174898-7174899
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:7163757..7166355-chr9:7173278..7174995,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1011341	0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10511462	0.81[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.87[ASN][1000 genomes]
rs10815533	0.88[ASN][1000 genomes]
rs1467700	0.83[AMR][1000 genomes]
rs1887871	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1887872	0.91[ASN][1000 genomes]
rs1928212	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1958344	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2026709	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2026714	0.82[EUR][1000 genomes]
rs2094613	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2248904	0.83[AMR][1000 genomes]
rs2381570	0.84[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2381572	0.83[AMR][1000 genomes]
rs2770728	0.91[ASN][1000 genomes]
rs2770729	0.92[ASN][1000 genomes]
rs2770730	0.91[ASN][1000 genomes]
rs2770731	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2770732	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2770733	0.90[ASN][1000 genomes]
rs2770734	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2770735	0.83[AMR][1000 genomes]
rs2770736	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2770737	0.83[AMR][1000 genomes]
rs2770741	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2770742	0.91[ASN][1000 genomes]
rs2770743	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2770744	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2770745	0.89[ASN][1000 genomes]
rs2770746	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2770747	0.83[ASN][1000 genomes]
rs2820918	0.88[ASN][1000 genomes]
rs2820919	0.84[ASN][1000 genomes]
rs2820920	0.91[ASN][1000 genomes]
rs2820922	0.83[AMR][1000 genomes]
rs2820923	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2820925	0.91[ASN][1000 genomes]
rs2820926	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2820927	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2820928	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2820929	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2820930	0.91[ASN][1000 genomes]
rs2820931	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2820934	0.95[ASN][1000 genomes]
rs3753002	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3753003	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7022054	0.83[ASW][hapmap];0.84[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7874501	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs913584	0.85[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs913587	0.83[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs913588	0.92[CEU][hapmap]
rs913589	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs913591	0.80[AMR][1000 genomes]
rs971380	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv613259	chr9:7032776-7541338	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1015874	chr9:7048807-7434890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv539971	chr9:7048807-7434890	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv892190	chr9:7094860-7186074	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv892192	chr9:7153009-7257340	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
8	nsv528873	chr9:7163530-7177936	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs913590	KDM4C	cis	brain	BrainEAC

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7148600-7185400	Weak transcription	HMEC	breast
2	chr9:7149600-7185400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr9:7149600-7186200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:7150400-7175800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:7151800-7188600	Weak transcription	Colonic Mucosa	Colon
6	chr9:7160800-7175200	Strong transcription	Primary B cells from cord blood	blood
7	chr9:7160800-7182000	Weak transcription	Dnd41	blood
8	chr9:7162600-7181600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr9:7162600-7182200	Weak transcription	Small Intestine	intestine
10	chr9:7163200-7177800	Strong transcription	Primary B cells from peripheral blood	blood
11	chr9:7163400-7180600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr9:7163800-7179000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr9:7164000-7176200	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr9:7164600-7178000	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr9:7165800-7176200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr9:7165800-7179400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr9:7165800-7183800	Weak transcription	Esophagus	oesophagus
18	chr9:7165800-7185400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr9:7166000-7175600	Weak transcription	Colon Smooth Muscle	Colon
20	chr9:7166200-7181000	Weak transcription	Hela-S3	cervix
21	chr9:7166400-7176800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:7167200-7185600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:7168200-7176400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:7169200-7183000	Strong transcription	Primary T cells from cord blood	blood
25	chr9:7169400-7176600	Strong transcription	Fetal Intestine Large	intestine
26	chr9:7169600-7175000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr9:7169600-7176400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr9:7169600-7176600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr9:7169600-7176800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr9:7169800-7176600	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr9:7169800-7176600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr9:7169800-7176800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr9:7169800-7177600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr9:7170000-7176400	Strong transcription	Adipose Nuclei	Adipose
35	chr9:7170000-7176400	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr9:7170800-7176600	Enhancers	Placenta	Placenta
37	chr9:7171000-7175000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:7171000-7175000	Enhancers	Placenta Amnion	Placenta Amnion
39	chr9:7171000-7176400	Strong transcription	Thymus	Thymus
40	chr9:7171200-7188200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr9:7171200-7193000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr9:7172000-7182400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr9:7172000-7183800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr9:7172200-7175000	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr9:7172200-7175400	Enhancers	Psoas Muscle	Psoas
46	chr9:7172200-7176600	Strong transcription	Fetal Intestine Small	intestine
47	chr9:7172600-7175000	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr9:7172600-7185400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr9:7172800-7176600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr9:7172800-7178600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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