Variant report

Variant	rs9307076
Chromosome Location	chr4:77027120-77027121
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	RAD21	chr4:77027036-77027215	K562	blood:	n/a	chr4:77027125-77027132 chr4:77027152-77027171
2	CTCF	chr4:77027039-77027226	MCF-7	breast:	n/a	chr4:77027155-77027171 chr4:77027149-77027170 chr4:77027156-77027169 chr4:77027154-77027172
3	CTCF	chr4:77027110-77027143	Gliobla	brain:	n/a	n/a
4	CTCF	chr4:77027040-77027190	HMEC	breast:	n/a	chr4:77027155-77027171 chr4:77027149-77027170 chr4:77027156-77027169 chr4:77027154-77027172
5	CTCF	chr4:77027095-77027282	GM12878	blood:	n/a	chr4:77027155-77027171 chr4:77027149-77027170 chr4:77027156-77027169 chr4:77027154-77027172
6	CTCF	chr4:77027000-77027150	HCPEpiC	choroid plexus:	n/a	n/a
7	CTCF	chr4:77027100-77027250	HEEpiC	esophagus:	n/a	chr4:77027155-77027171 chr4:77027149-77027170 chr4:77027156-77027169 chr4:77027154-77027172
8	CTCF	chr4:77027040-77027190	K562	blood:	n/a	chr4:77027155-77027171 chr4:77027149-77027170 chr4:77027156-77027169 chr4:77027154-77027172
9	CTCF	chr4:77027001-77027212	K562	blood:	n/a	chr4:77027155-77027171 chr4:77027149-77027170 chr4:77027156-77027169 chr4:77027154-77027172
10	CTCF	chr4:77027080-77027230	HCT-116	colon:	n/a	chr4:77027155-77027171 chr4:77027149-77027170 chr4:77027156-77027169 chr4:77027154-77027172
11	CTCF	chr4:77027080-77027230	HMEC	breast:	n/a	chr4:77027155-77027171 chr4:77027149-77027170 chr4:77027156-77027169 chr4:77027154-77027172
12	CTCF	chr4:77027064-77027125	LNCaP	prostate:	n/a	n/a
13	CTCF	chr4:77027038-77027298	K562	blood:	n/a	chr4:77027155-77027171 chr4:77027149-77027170 chr4:77027156-77027169 chr4:77027154-77027172
14	CTCF	chr4:77027073-77027238	Hela-S3	cervix:	n/a	chr4:77027155-77027171 chr4:77027149-77027170 chr4:77027156-77027169 chr4:77027154-77027172
15	CTCF	chr4:77027100-77027207	K562	blood:	n/a	chr4:77027155-77027171 chr4:77027149-77027170 chr4:77027156-77027169 chr4:77027154-77027172
16	CTCF	chr4:77027040-77027190	MCF-7	breast:	n/a	chr4:77027155-77027171 chr4:77027149-77027170 chr4:77027156-77027169 chr4:77027154-77027172
17	CTCF	chr4:77026996-77027339	K562	blood:	n/a	chr4:77027155-77027171 chr4:77027149-77027170 chr4:77027156-77027169 chr4:77027154-77027172
18	CTCF	chr4:77027062-77027213	MCF-7	breast:	n/a	chr4:77027155-77027171 chr4:77027149-77027170 chr4:77027156-77027169 chr4:77027154-77027172
19	CTCF	chr4:77027080-77027230	HCPEpiC	choroid plexus:	n/a	chr4:77027155-77027171 chr4:77027149-77027170 chr4:77027156-77027169 chr4:77027154-77027172
20	RAD21	chr4:77027060-77027220	Hela-S3	cervix:	n/a	chr4:77027125-77027132 chr4:77027152-77027171

No.	Distal block	Cell Line	Cell type
1	chr4:76917060..76917634-chr4:77026735..77027377,3	MCF-7	breast:
2	chr4:77024140..77027603-chr4:77067488..77070849,3	K562	blood:
3	chr4:76916674..76917591-chr4:77026390..77027328,2	K562	blood:

Variant related genes	Relation type
ART3	TF binding region
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10008834	0.93[GIH][hapmap]
rs10014749	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10015467	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10015842	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10028141	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11097230	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11944608	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12331871	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13115827	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13131187	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13141895	0.93[GIH][hapmap]
rs13152491	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17001385	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17001393	0.95[YRI][hapmap];0.95[AFR][1000 genomes]
rs17001395	0.95[YRI][hapmap];0.95[AFR][1000 genomes]
rs17001396	0.80[AFR][1000 genomes]
rs17001398	1.00[ASW][hapmap];0.88[LWK][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes]
rs2197104	0.90[EUR][1000 genomes]
rs28600676	0.91[EUR][1000 genomes]
rs28611472	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28628345	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28635901	0.91[EUR][1000 genomes]
rs28649343	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28726273	0.89[EUR][1000 genomes]
rs28857291	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28894799	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34019987	0.87[EUR][1000 genomes]
rs34023726	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34067866	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34072573	0.86[EUR][1000 genomes]
rs3816248	0.89[GIH][hapmap]
rs4241585	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4241586	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4263427	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4339237	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4515186	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4552491	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4859609	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs6532189	0.96[GIH][hapmap]
rs6829592	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9307078	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1009047	chr4:76989180-77077885	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9307076	CDKL2	cis	cerebellum	SCAN
rs9307076	CXCL10	cis	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77017000-77034400	Weak transcription	Right Ventricle	heart
2	chr4:77024000-77032200	Weak transcription	Left Ventricle	heart
3	chr4:77026200-77027800	Enhancers	Fetal Brain Male	brain
4	chr4:77026200-77027800	Weak transcription	K562	blood
5	chr4:77026200-77028000	Enhancers	Brain Cingulate Gyrus	brain
6	chr4:77026400-77027200	Enhancers	Brain Anterior Caudate	brain
7	chr4:77026400-77027800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr4:77026400-77027800	Enhancers	Brain Angular Gyrus	brain
9	chr4:77026400-77033400	Weak transcription	HSMMtube	muscle
10	chr4:77026600-77027200	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr4:77026600-77027600	Enhancers	Brain Hippocampus Middle	brain
12	chr4:77026600-77027600	Enhancers	Brain Substantia Nigra	brain
13	chr4:77026600-77033400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr4:77026800-77027600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:77026800-77027600	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr4:77027000-77027200	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr4:77027000-77027200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:77027000-77027200	Enhancers	Fetal Muscle Leg	muscle
19	chr4:77027000-77027200	Enhancers	Right Atrium	heart
20	chr4:77027000-77027600	Weak transcription	Fetal Brain Female	brain
21	chr4:77027000-77028400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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