Variant report

Variant	rs7872123
Chromosome Location	chr9:96716158-96716159
allele	C/T
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	SUZ12	chr9:96709708-96717433	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr9:96715218-96716678	H1-neurons	neurons:	n/a	n/a
3	CTBP2	chr9:96710652-96717425	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr9:96715057-96716383	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96709646..96715968-chr9:96715980..96721050,10	MCF-7	breast:
2	chr9:96713619..96716485-chr9:96717370..96719166,2	K562	blood:

Variant related genes	Relation type
ENSG00000235601	TF binding region
BARX1	TF binding region
ENSG00000235601	Chromatin interaction
ENSG00000131668	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1057713	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10821273	0.96[CEU][hapmap];0.83[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10821274	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11788035	0.96[CEU][hapmap];0.89[CHB][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11999521	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11999551	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12005806	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1320546	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13283836	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13291289	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1933680	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1933681	0.83[CHB][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1933682	0.84[AMR][1000 genomes]
rs2095778	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35001304	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4437716	0.96[CEU][hapmap];0.83[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4563951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56285369	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7034685	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv824993	chr9:96699362-96725105	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893590	chr9:96701287-96729129	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3442102	chr9:96716156-96718704	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7872123	ORMDL2	trans	parietal	SCAN
rs7872123	SPTLC1	cis	cerebellum	SCAN
rs7872123	WNK2	cis	cerebellum	SCAN
rs7872123	IPPK	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96713000-96717000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
2	chr9:96713200-96716400	Bivalent Enhancer	Fetal Brain Male	brain
3	chr9:96713600-96716400	Weak transcription	Hela-S3	cervix
4	chr9:96713800-96716400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
5	chr9:96713800-96716600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
6	chr9:96713800-96716800	Bivalent Enhancer	Brain Germinal Matrix	brain
7	chr9:96713800-96716800	Bivalent Enhancer	Brain Substantia Nigra	brain
8	chr9:96713800-96717000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr9:96713800-96717200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
10	chr9:96713800-96717400	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr9:96713800-96717800	Bivalent Enhancer	Liver	Liver
12	chr9:96713800-96718400	Bivalent Enhancer	Lung	lung
13	chr9:96714200-96716200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
14	chr9:96714200-96716400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
15	chr9:96714200-96716600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:96714200-96717200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
17	chr9:96714200-96717400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr9:96714200-96717800	Enhancers	Pancreas	Pancrea
19	chr9:96714400-96716200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
20	chr9:96714400-96717000	Bivalent Enhancer	Adipose Nuclei	Adipose
21	chr9:96714400-96717200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
22	chr9:96714600-96716400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
23	chr9:96714600-96716800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:96714600-96716800	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
25	chr9:96714600-96717000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
26	chr9:96714600-96717000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:96714600-96717000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:96714800-96716200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
29	chr9:96714800-96716800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
30	chr9:96715000-96716200	Weak transcription	Osteobl	bone
31	chr9:96715000-96716400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
32	chr9:96715000-96716400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr9:96715000-96717000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
34	chr9:96715000-96718800	Bivalent Enhancer	Spleen	Spleen
35	chr9:96715200-96716200	Bivalent/Poised TSS	Fetal Stomach	stomach
36	chr9:96715400-96716200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
37	chr9:96715400-96716600	Bivalent Enhancer	Colonic Mucosa	Colon
38	chr9:96715400-96716800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
39	chr9:96715400-96717200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
40	chr9:96715600-96716400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
41	chr9:96715800-96716200	Bivalent Enhancer	Colon Smooth Muscle	Colon
42	chr9:96715800-96716200	Active TSS	Gastric	stomach
43	chr9:96715800-96716400	Bivalent Enhancer	Fetal Heart	heart
44	chr9:96715800-96716400	Bivalent Enhancer	Right Ventricle	heart
45	chr9:96715800-96716600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:96715800-96717000	Bivalent Enhancer	Brain Hippocampus Middle	brain
47	chr9:96715800-96717000	Weak transcription	Right Atrium	heart
48	chr9:96715800-96717200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr9:96715800-96717200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:96716000-96716200	Bivalent Enhancer	Fetal Brain Female	brain

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