Variant report

Variant	rs946929
Chromosome Location	chr9:6997639-6997640
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	chr9:6996659..6998506-chr9:6999056..7001855,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10975962	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11790877	0.89[CEU][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7020065	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7847191	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7854608	0.82[CEU][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7866390	0.81[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs946929	JMJD2C	Cis_1M	lymphoblastoid	RTeQTL
rs946929	SLC1A1	cis	cerebellum	SCAN

Chromatin state (count:114 , 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	chr9:6974200-6999800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:6976200-7011800	Weak transcription	Psoas Muscle	Psoas
4	chr9:6977000-7008200	Strong transcription	Primary B cells from cord blood	blood
5	chr9:6977600-6999200	Strong transcription	Primary T cells from cord blood	blood
6	chr9:6977800-7008200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:6978800-7008200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:6979600-6997800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr9:6979600-6998200	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr9:6979600-7008000	Weak transcription	NHEK	skin
11	chr9:6979800-7018600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr9:6980200-6998000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr9:6980200-7008400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr9:6980800-7004200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr9:6981000-6997800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr9:6981000-6998200	Strong transcription	Fetal Thymus	thymus
17	chr9:6981400-7008000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:6981400-7011200	Weak transcription	HUVEC	blood vessel
19	chr9:6981600-6999000	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr9:6982600-6998800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:6982600-7000200	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr9:6982600-7008200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:6982600-7008200	Weak transcription	NHLF	lung
24	chr9:6982800-7004200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr9:6983000-7008600	Weak transcription	Fetal Brain Female	brain
26	chr9:6983400-7010200	Weak transcription	Stomach Mucosa	stomach
27	chr9:6983800-7008200	Weak transcription	A549	lung
28	chr9:6984000-7018200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr9:6985200-7007800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr9:6985200-7008200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:6985600-7008000	Weak transcription	K562	blood
32	chr9:6985600-7008200	Weak transcription	Right Ventricle	heart
33	chr9:6985600-7008400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr9:6985600-7011200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr9:6985600-7019200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr9:6985600-7035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr9:6986800-7015600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr9:6987200-7008000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr9:6987200-7008000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr9:6987200-7008200	Weak transcription	Colon Smooth Muscle	Colon
41	chr9:6987200-7008200	Weak transcription	NHDF-Ad	bronchial
42	chr9:6987200-7008400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr9:6987400-7008000	Weak transcription	Brain Angular Gyrus	brain
44	chr9:6987400-7008600	Weak transcription	Hela-S3	cervix
45	chr9:6987600-7008000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:6987600-7008000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:6987600-7008000	Weak transcription	Fetal Muscle Leg	muscle
48	chr9:6987600-7008000	Weak transcription	HepG2	liver
49	chr9:6987600-7008200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr9:6987600-7008400	Weak transcription	Osteobl	bone

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