Variant report

Variant	rs2269310
Chromosome Location	chr14:65237203-65237204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:65236406..65238407-chr14:65243538..65245205,2	MCF-7	breast:
2	chr14:65228571..65230155-chr14:65235739..65238455,2	K562	blood:
3	chr14:65235455..65238198-chr14:65239523..65242367,2	K562	blood:
4	chr14:64968342..64970352-chr14:65235886..65238559,2	MCF-7	breast:
5	chr14:65227919..65230155-chr14:65235739..65238455,3	K562	blood:
6	chr14:65230521..65233110-chr14:65236260..65237883,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070182	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs170681	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs229592	0.87[CHB][hapmap]
rs229596	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs92070	0.81[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818582	chr14:65172898-65256685	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1035833	chr14:65176371-65246181	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv1801406	chr14:65193725-65264416	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
4	nsv902023	chr14:65200821-65243885	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv902024	chr14:65200821-65244950	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv902025	chr14:65229364-65246181	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv519823	chr14:65230059-65241933	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2269310	SIX4	cis	cerebellum	SCAN
rs2269310	SLC38A6	cis	parietal	SCAN
rs2269310	GPHB5	cis	parietal	SCAN
rs2269310	RAD51L1	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65228400-65265000	Weak transcription	Aorta	Aorta
2	chr14:65229600-65246200	Weak transcription	Psoas Muscle	Psoas
3	chr14:65230600-65237800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr14:65231600-65242400	Strong transcription	Right Ventricle	heart
5	chr14:65231600-65244000	Strong transcription	Skeletal Muscle Male	skeletal muscle
6	chr14:65231600-65244400	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr14:65231600-65250600	Weak transcription	Brain Angular Gyrus	brain
8	chr14:65231600-65250600	Weak transcription	Brain Anterior Caudate	brain
9	chr14:65231600-65261400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr14:65232000-65246000	Weak transcription	Pancreas	Pancrea
11	chr14:65232200-65239400	Weak transcription	Brain Hippocampus Middle	brain
12	chr14:65232200-65244600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr14:65232200-65274200	Weak transcription	Gastric	stomach
14	chr14:65232400-65237800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr14:65232600-65237400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr14:65232600-65242600	Strong transcription	K562	blood
17	chr14:65233000-65265600	Weak transcription	Fetal Brain Male	brain
18	chr14:65233600-65237400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr14:65233600-65242400	Strong transcription	Left Ventricle	heart
20	chr14:65234800-65241000	Weak transcription	Spleen	Spleen
21	chr14:65235600-65237400	Genic enhancers	Fetal Muscle Trunk	muscle
22	chr14:65235600-65239800	Strong transcription	Brain Germinal Matrix	brain
23	chr14:65236000-65237400	Weak transcription	Fetal Brain Female	brain
24	chr14:65236000-65239400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr14:65236000-65239600	Weak transcription	Fetal Heart	heart
26	chr14:65236200-65239200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr14:65236200-65239600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr14:65236400-65237400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr14:65237000-65239000	Enhancers	Primary T cells from cord blood	blood
30	chr14:65237000-65239200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr14:65237000-65242600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr14:65237200-65237600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr14:65237200-65239200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr14:65237200-65240000	Strong transcription	Fetal Muscle Leg	muscle

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