Variant report

Variant	rs4744175
Chromosome Location	chr9:95869726-95869727
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	CTCF	chr9:95869580-95869730	MCF-7	breast:	n/a	chr9:95869642-95869650 chr9:95869642-95869655

No.	Distal block	Cell Line	Cell type
1	chr9:95855552..95862102-chr9:95867626..95876894,17	K562	blood:
2	chr9:95869193..95869900-chr9:96067217..96067753,2	MCF-7	breast:
3	chr9:95855712..95863110-chr9:95867626..95874665,14	K562	blood:
4	chr9:95765978..95766635-chr9:95868909..95869887,2	MCF-7	breast:
5	chr9:95855064..95861522-chr9:95867449..95872462,10	MCF-7	breast:

Variant related genes	Relation type
C9orf89	TF binding region
ENSG00000165233	Chromatin interaction
ENSG00000223446	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10739942	0.96[ASN][1000 genomes]
rs10761193	0.96[ASN][1000 genomes]
rs10821067	0.96[ASN][1000 genomes]
rs10821070	0.85[ASN][1000 genomes]
rs10821071	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1123000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1539672	0.96[ASN][1000 genomes]
rs2027585	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2298242	0.97[ASN][1000 genomes]
rs2298243	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3819011	0.98[ASN][1000 genomes]
rs4077822	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4237219	0.99[ASN][1000 genomes]
rs4333675	0.98[ASN][1000 genomes]
rs4384040	0.97[ASN][1000 genomes]
rs4743882	1.00[ASN][1000 genomes]
rs4743883	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4743884	0.82[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4743885	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4743887	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744171	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4744172	0.99[ASN][1000 genomes]
rs4744174	0.99[ASN][1000 genomes]
rs4744176	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7020130	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7857595	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4744175	NINJ1	cis	multi-tissue	Pritchard

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95859400-95876200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:95859600-95889400	Weak transcription	Fetal Kidney	kidney
3	chr9:95860200-95872600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:95860400-95876400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr9:95860800-95872800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:95861000-95869800	Weak transcription	Aorta	Aorta
7	chr9:95861600-95872200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:95861800-95869800	Weak transcription	Fetal Intestine Large	intestine
9	chr9:95861800-95869800	Weak transcription	HepG2	liver
10	chr9:95861800-95882000	Weak transcription	HSMMtube	muscle
11	chr9:95862000-95870600	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:95862000-95871200	Weak transcription	Hela-S3	cervix
13	chr9:95862000-95872800	Weak transcription	Osteobl	bone
14	chr9:95862000-95873800	Weak transcription	NH-A	brain
15	chr9:95862000-95878400	Weak transcription	Stomach Mucosa	stomach
16	chr9:95862000-95881800	Weak transcription	HUVEC	blood vessel
17	chr9:95862200-95869800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr9:95862200-95869800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr9:95862200-95869800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr9:95862200-95870000	Weak transcription	Right Ventricle	heart
21	chr9:95862200-95870800	Weak transcription	Pancreas	Pancrea
22	chr9:95862200-95870800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr9:95862200-95871600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:95862200-95878000	Weak transcription	HSMM	muscle
25	chr9:95862200-95878600	Weak transcription	Psoas Muscle	Psoas
26	chr9:95862200-95878600	Weak transcription	Right Atrium	heart
27	chr9:95862400-95869800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:95862400-95869800	Weak transcription	NHEK	skin
29	chr9:95862400-95870000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:95862400-95870000	Weak transcription	Adipose Nuclei	Adipose
31	chr9:95862400-95870000	Weak transcription	Left Ventricle	heart
32	chr9:95862400-95873000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr9:95862600-95870000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:95862600-95870000	Weak transcription	Brain Angular Gyrus	brain
35	chr9:95862600-95870800	Weak transcription	Ovary	ovary
36	chr9:95862800-95869800	Weak transcription	Brain Hippocampus Middle	brain
37	chr9:95862800-95869800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr9:95862800-95869800	Weak transcription	Lung	lung
39	chr9:95862800-95870000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr9:95862800-95870200	Weak transcription	Brain Anterior Caudate	brain
41	chr9:95862800-95871200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr9:95864200-95871600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr9:95865000-95870200	Weak transcription	A549	lung
44	chr9:95866200-95870200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:95866400-95869800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr9:95866600-95869800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr9:95866600-95878600	Weak transcription	NHDF-Ad	bronchial
48	chr9:95866800-95869800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr9:95866800-95869800	Weak transcription	Brain Substantia Nigra	brain
50	chr9:95866800-95869800	Weak transcription	Rectal Mucosa Donor 31	rectum

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