Variant report

Variant	rs12375685
Chromosome Location	chr9:7020864-7020865
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:35003633..35004245-chr9:7020432..7021432,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10758817	0.88[EUR][1000 genomes]
rs10758818	0.88[EUR][1000 genomes]
rs10758819	0.87[EUR][1000 genomes]
rs10758821	0.83[EUR][1000 genomes]
rs10815507	0.88[EUR][1000 genomes]
rs10975971	0.84[ASN][1000 genomes]
rs10975984	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10975991	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10975992	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10975995	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12380879	0.85[ASN][1000 genomes]
rs1407862	0.81[EUR][1000 genomes]
rs2031198	0.82[EUR][1000 genomes]
rs4742281	0.82[ASN][1000 genomes]
rs4742283	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7848038	0.89[ASN][1000 genomes]
rs7853037	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7858749	0.90[EUR][1000 genomes]
rs7860217	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv613257	chr9:7015330-7037370	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12375685	JMJD2C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6985600-7035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr9:7008800-7024200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr9:7009000-7021600	Weak transcription	HMEC	breast
4	chr9:7009000-7026200	Weak transcription	A549	lung
5	chr9:7009000-7027400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr9:7009000-7027800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:7009000-7027800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr9:7009000-7028400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:7009000-7030400	Weak transcription	NHEK	skin
10	chr9:7009000-7044800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:7009000-7046200	Weak transcription	Small Intestine	intestine
12	chr9:7009000-7055200	Weak transcription	K562	blood
13	chr9:7009000-7056400	Weak transcription	Brain Substantia Nigra	brain
14	chr9:7009000-7076600	Weak transcription	HSMM	muscle
15	chr9:7009200-7077600	Weak transcription	Osteobl	bone
16	chr9:7009400-7029600	Weak transcription	Hela-S3	cervix
17	chr9:7009400-7042000	Weak transcription	NHDF-Ad	bronchial
18	chr9:7009800-7076600	Weak transcription	HSMMtube	muscle
19	chr9:7011000-7021000	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr9:7011800-7048800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr9:7012200-7027400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:7012200-7027400	Weak transcription	Brain Anterior Caudate	brain
23	chr9:7012200-7027400	Weak transcription	Right Ventricle	heart
24	chr9:7012200-7027400	Weak transcription	Spleen	Spleen
25	chr9:7012200-7027600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:7012200-7046800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr9:7012200-7052600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr9:7012200-7111200	Weak transcription	Colonic Mucosa	Colon
29	chr9:7012400-7028000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr9:7012800-7027600	Weak transcription	Esophagus	oesophagus
31	chr9:7012800-7028400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr9:7012800-7048800	Weak transcription	Dnd41	blood
33	chr9:7012800-7076800	Weak transcription	Pancreas	Pancrea
34	chr9:7013800-7031800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr9:7014200-7027400	Weak transcription	Ovary	ovary
36	chr9:7014600-7048000	Weak transcription	Colon Smooth Muscle	Colon
37	chr9:7016000-7025200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:7016000-7036400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr9:7016200-7033200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr9:7016800-7021000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr9:7016800-7027600	Weak transcription	Fetal Stomach	stomach
42	chr9:7017000-7027200	Weak transcription	Aorta	Aorta
43	chr9:7017000-7027600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr9:7017200-7026000	Weak transcription	Fetal Intestine Small	intestine
45	chr9:7017200-7026600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr9:7017200-7027200	Weak transcription	Gastric	stomach
47	chr9:7017200-7028200	Weak transcription	Left Ventricle	heart
48	chr9:7017200-7028400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr9:7017200-7028800	Weak transcription	Fetal Muscle Leg	muscle
50	chr9:7017400-7027400	Weak transcription	Fetal Muscle Trunk	muscle

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