Variant report

Variant	rs11840407
Chromosome Location	chr13:80053169-80053170
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	SPI1	chr13:80053086-80053471	HL-60	blood:	n/a	n/a
2	SPI1	chr13:80053122-80053369	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:80052830..80055109-chr7:8301412..8303187,2	MCF-7	breast:

Variant related genes	Relation type
NDFIP2	TF binding region
ENSG00000003147	Chromatin interaction
ENSG00000229970	Chromatin interaction
ENSG00000244239	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11838700	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11838897	1.00[EUR][1000 genomes]
rs11839689	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11841482	1.00[EUR][1000 genomes]
rs11841756	1.00[ASN][1000 genomes]
rs11841968	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11843203	1.00[EUR][1000 genomes]
rs11843917	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11843939	1.00[EUR][1000 genomes]
rs1335372	1.00[ASN][1000 genomes]
rs17071492	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17071589	1.00[ASN][1000 genomes]
rs17071629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17431002	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs35724140	1.00[EUR][1000 genomes]
rs41364649	1.00[CEU][hapmap]
rs4884132	1.00[ASN][1000 genomes]
rs4885635	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4885639	1.00[ASN][1000 genomes]
rs4885641	1.00[ASN][1000 genomes]
rs55820419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56863569	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58069884	1.00[ASN][1000 genomes]
rs58233612	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58264675	1.00[ASN][1000 genomes]
rs59251364	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59319360	1.00[ASN][1000 genomes]
rs60016606	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67435118	1.00[ASN][1000 genomes]
rs7139902	1.00[ASN][1000 genomes]
rs73235960	1.00[ASN][1000 genomes]
rs7325970	1.00[ASN][1000 genomes]
rs7337908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7338662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548905	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548913	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548931	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548932	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548936	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548939	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548952	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548962	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548974	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73551514	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73551516	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74098308	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74098315	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74098399	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7983312	1.00[ASN][1000 genomes]
rs7985220	1.00[ASN][1000 genomes]
rs7985239	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985291	1.00[ASN][1000 genomes]
rs7991663	1.00[ASN][1000 genomes]
rs7992646	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7994370	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7995350	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7995408	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7995717	1.00[ASN][1000 genomes]
rs7996153	1.00[EUR][1000 genomes]
rs8000301	1.00[CHB][hapmap]
rs8002638	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9530927	1.00[CHB][hapmap]
rs9530936	1.00[ASN][1000 genomes]
rs9545126	1.00[CHB][hapmap]
rs9545129	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9545132	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9545143	1.00[ASN][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	nsv832657	chr13:79904978-80099108	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv523979	chr13:79979679-80120263	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80048400-80053600	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr13:80050400-80054800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr13:80052000-80053200	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr13:80052000-80053200	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr13:80052400-80053200	Enhancers	Brain Hippocampus Middle	brain
6	chr13:80052400-80054800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr13:80052400-80054800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr13:80052400-80054800	Weak transcription	HMEC	breast
9	chr13:80052600-80054800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:80052600-80054800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr13:80052600-80054800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr13:80052600-80054800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr13:80052600-80054800	Weak transcription	NHEK	skin
14	chr13:80052800-80053600	Weak transcription	HepG2	liver
15	chr13:80052800-80054600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr13:80052800-80054600	Weak transcription	Brain Anterior Caudate	brain
17	chr13:80052800-80054800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr13:80052800-80054800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr13:80052800-80054800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr13:80052800-80055000	Weak transcription	Psoas Muscle	Psoas
21	chr13:80053000-80053200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
22	chr13:80053000-80053400	Enhancers	Fetal Heart	heart
23	chr13:80053000-80053600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
24	chr13:80053000-80054600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr13:80053000-80054800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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