Variant report

Variant	rs4077822
Chromosome Location	chr9:95859739-95859740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr9:95858921-95860509	HEK293-T-REx	kidney:	n/a	chr9:95859281-95859290
2	EBF1	chr9:95859501-95860068	GM12878	blood:	n/a	chr9:95859916-95859927 chr9:95859918-95859927

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:95855712..95863110-chr9:95867626..95874665,14	K562	blood:
2	chr9:95858239..95860012-chr9:96214576..96216562,2	MCF-7	breast:
3	chr9:95855662..95862507-chr9:95894736..95899302,16	MCF-7	breast:
4	chr9:95857571..95862229-chr9:96211597..96216359,5	K562	blood:
5	chr9:95816364..95826268-chr9:95852309..95863275,20	MCF-7	breast:
6	chr9:95856800..95859803-chr9:96212504..96215667,3	MCF-7	breast:
7	chr9:95855064..95861522-chr9:95867449..95872462,10	MCF-7	breast:
8	chr9:95855552..95862102-chr9:95867626..95876894,17	K562	blood:
9	chr9:95818697..95822651-chr9:95855885..95860349,6	MCF-7	breast:
10	chr9:95856253..95862485-chr9:95892353..95899486,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000223446	TF binding region
ENSG00000157303	Chromatin interaction
ENSG00000188938	Chromatin interaction
ENSG00000131669	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000165233	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10739942	0.96[ASN][1000 genomes]
rs10761193	0.96[ASN][1000 genomes]
rs10821067	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821069	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10821070	0.85[ASN][1000 genomes]
rs10821071	0.95[ASN][1000 genomes]
rs1123000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1539672	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2027585	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2298242	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3819011	0.98[ASN][1000 genomes]
rs4237219	0.99[ASN][1000 genomes]
rs4333675	0.98[ASN][1000 genomes]
rs4384040	0.97[ASN][1000 genomes]
rs4743882	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743883	1.00[ASN][1000 genomes]
rs4743884	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4743885	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4743887	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4744171	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744172	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744174	0.99[ASN][1000 genomes]
rs4744175	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4744176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7020130	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857595	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1054767	chr9:95738134-95875977	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Strong transcription 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	22 gene(s)	inside rSNPs	diseases
3	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv893577	chr9:95812707-95872216	Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv893578	chr9:95818641-95887320	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv893579	chr9:95855100-95923091	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	esv3346305	chr9:95857306-95859804	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	esv3441183	chr9:95857356-95859904	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4077822	C9orf89	cis	Esophagus Mucosa	GTEx
rs4077822	C9orf89	cis	cerebellum	SCAN
rs4077822	C9orf89	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95857400-95859800	Active TSS	H9 Cell Line	embryonic stem cell
2	chr9:95857800-95859800	Active TSS	NHLF	lung
3	chr9:95858600-95861000	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr9:95858600-95861000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr9:95858800-95859800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
6	chr9:95858800-95860200	Flanking Active TSS	Fetal Brain Male	brain
7	chr9:95858800-95860400	Flanking Active TSS	Dnd41	blood
8	chr9:95858800-95861000	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr9:95858800-95861000	Flanking Active TSS	Colonic Mucosa	Colon
10	chr9:95858800-95861200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr9:95858800-95861200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr9:95858800-95861800	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr9:95859000-95859800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr9:95859000-95859800	Flanking Active TSS	Fetal Heart	heart
15	chr9:95859000-95859800	Flanking Active TSS	Fetal Muscle Trunk	muscle
16	chr9:95859000-95859800	Flanking Active TSS	Fetal Muscle Leg	muscle
17	chr9:95859000-95860000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr9:95859000-95860000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:95859000-95860000	Flanking Active TSS	Fetal Thymus	thymus
20	chr9:95859000-95860400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr9:95859000-95861000	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr9:95859000-95861000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr9:95859000-95861000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr9:95859000-95861000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr9:95859000-95861000	Flanking Active TSS	Hela-S3	cervix
26	chr9:95859000-95861000	Flanking Active TSS	HSMMtube	muscle
27	chr9:95859000-95861000	Flanking Active TSS	HUVEC	blood vessel
28	chr9:95859000-95861000	Flanking Active TSS	NHEK	skin
29	chr9:95859000-95861200	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr9:95859000-95861200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr9:95859000-95861200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr9:95859000-95861200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
33	chr9:95859000-95861200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:95859000-95861200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr9:95859000-95861400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr9:95859000-95861800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr9:95859000-95862000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr9:95859000-95862800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:95859000-95862800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:95859200-95859800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
41	chr9:95859200-95859800	Flanking Active TSS	Esophagus	oesophagus
42	chr9:95859200-95859800	Flanking Active TSS	Fetal Intestine Small	intestine
43	chr9:95859200-95859800	Flanking Active TSS	Left Ventricle	heart
44	chr9:95859200-95859800	Flanking Active TSS	Stomach Mucosa	stomach
45	chr9:95859200-95860000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr9:95859200-95860000	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr9:95859200-95860000	Flanking Active TSS	Thymus	Thymus
48	chr9:95859200-95860000	Flanking Active TSS	NH-A	brain
49	chr9:95859200-95860200	Flanking Active TSS	Fetal Brain Female	brain
50	chr9:95859200-95860400	Flanking Active TSS	Brain Substantia Nigra	brain

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