Variant report

Variant	rs10975971
Chromosome Location	chr9:7010239-7010240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:7010058-7010341	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
KDM4C	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10815509	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs10975984	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs10975991	0.87[ASN][1000 genomes]
rs10975992	1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs10975995	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs12375685	0.84[ASN][1000 genomes]
rs12380879	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1407855	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs2890733	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2890736	0.81[CEU][hapmap]
rs3802404	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4742281	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742282	0.83[EUR][1000 genomes]
rs4742283	0.92[ASN][1000 genomes]
rs7848038	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7853037	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs7856928	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870402	chr9:6565246-7016784	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1033539	chr9:6566610-7022554	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv466111	chr9:6567841-7017391	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
4	nsv613208	chr9:6567841-7017391	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv1024831	chr9:6573752-7018641	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
6	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
7	nsv892181	chr9:6680477-7070962	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
8	nsv613252	chr9:6715730-7022554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	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
10	nsv1023461	chr9:6774993-7022554	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv831501	chr9:6868099-7058526	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv892185	chr9:6929053-7070962	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1021234	chr9:6933222-7015397	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv870178	chr9:6941584-7060029	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv892186	chr9:6942605-7075305	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv892187	chr9:6974101-7035727	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv949711	chr9:6994399-7045058	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv892188	chr9:6999846-7026860	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10975971	JMJD2C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6972000-7013200	Weak transcription	Fetal Kidney	kidney
2	chr9:6976200-7011800	Weak transcription	Psoas Muscle	Psoas
3	chr9:6979800-7018600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:6981400-7011200	Weak transcription	HUVEC	blood vessel
5	chr9:6984000-7018200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:6985600-7011200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr9:6985600-7019200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:6985600-7035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:6986800-7015600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr9:6998000-7010400	Weak transcription	Fetal Heart	heart
11	chr9:7003400-7012800	Weak transcription	Brain Germinal Matrix	brain
12	chr9:7003600-7010400	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr9:7007800-7019000	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr9:7008000-7010800	Strong transcription	Liver	Liver
15	chr9:7008000-7014200	Strong transcription	Adipose Nuclei	Adipose
16	chr9:7008000-7018800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr9:7008000-7018800	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr9:7008200-7014200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:7008200-7014800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:7008400-7011200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr9:7008600-7016000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:7008800-7010400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:7008800-7010400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr9:7008800-7011600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr9:7008800-7017000	Weak transcription	NHLF	lung
26	chr9:7008800-7024200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:7009000-7010600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr9:7009000-7011400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr9:7009000-7011400	Weak transcription	Aorta	Aorta
30	chr9:7009000-7011400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr9:7009000-7011600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:7009000-7011600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr9:7009000-7011600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:7009000-7011600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:7009000-7011600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr9:7009000-7011600	Weak transcription	Colon Smooth Muscle	Colon
37	chr9:7009000-7011600	Weak transcription	Esophagus	oesophagus
38	chr9:7009000-7011600	Weak transcription	Fetal Intestine Small	intestine
39	chr9:7009000-7011600	Weak transcription	Pancreas	Pancrea
40	chr9:7009000-7011600	Weak transcription	Thymus	Thymus
41	chr9:7009000-7011600	Weak transcription	Spleen	Spleen
42	chr9:7009000-7011800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:7009000-7011800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr9:7009000-7011800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr9:7009000-7011800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr9:7009000-7011800	Weak transcription	Fetal Muscle Leg	muscle
47	chr9:7009000-7011800	Weak transcription	Fetal Stomach	stomach
48	chr9:7009000-7011800	Weak transcription	Ovary	ovary
49	chr9:7009000-7011800	Weak transcription	Right Ventricle	heart
50	chr9:7009000-7015800	Weak transcription	Gastric	stomach

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