Variant report

Variant	rs9579401
Chromosome Location	chr13:30125811-30125812
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:30125675..30127526-chr13:30168701..30170678,2	MCF-7	breast:
2	chr13:30124978..30127325-chr13:30144094..30146175,2	MCF-7	breast:
3	chr13:30124073..30126477-chr13:30167606..30170454,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139514	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10220050	1.00[CEU][hapmap]
rs10454589	0.82[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10454590	0.91[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12868663	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17602182	1.00[ASN][1000 genomes]
rs2669038	1.00[CEU][hapmap]
rs34831702	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478085	0.84[CEU][hapmap];0.93[GIH][hapmap]
rs555913	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap]
rs7328329	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998704	1.00[CEU][hapmap]
rs819388	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9314960	1.00[CEU][hapmap]
rs9314962	1.00[CEU][hapmap]
rs9578104	1.00[CHD][hapmap]
rs9578106	0.91[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9578107	0.90[CEU][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579383	1.00[CHD][hapmap];0.92[GIH][hapmap]
rs9579384	1.00[CHD][hapmap];0.93[GIH][hapmap]
rs9579386	1.00[CHD][hapmap];0.93[GIH][hapmap]
rs9579388	1.00[CHD][hapmap];0.86[GIH][hapmap]
rs9579389	1.00[CHD][hapmap];0.93[GIH][hapmap]
rs9579390	1.00[CHD][hapmap];0.93[GIH][hapmap]
rs9579393	1.00[CHD][hapmap];0.93[GIH][hapmap]
rs9579398	0.91[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579399	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579400	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579402	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579403	0.96[EUR][1000 genomes]
rs9579404	0.96[EUR][1000 genomes]
rs9579405	0.89[CEU][hapmap]
rs9579406	1.00[CEU][hapmap]
rs9579407	1.00[CEU][hapmap]
rs9579408	1.00[CEU][hapmap]
rs9579410	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv979	chr13:30122254-30167821	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30071000-30128800	Strong transcription	Dnd41	blood
2	chr13:30092200-30133000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr13:30097200-30138400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr13:30098800-30129000	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr13:30103800-30137200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:30104200-30135400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr13:30105200-30136800	Weak transcription	Brain Germinal Matrix	brain
8	chr13:30107400-30129200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr13:30110400-30127200	Weak transcription	Brain Angular Gyrus	brain
10	chr13:30112800-30127200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr13:30112800-30129200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr13:30113200-30141600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr13:30113600-30129200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr13:30113800-30136200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr13:30114400-30126000	Weak transcription	Colon Smooth Muscle	Colon
16	chr13:30117800-30129000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr13:30119200-30128000	Strong transcription	HepG2	liver
18	chr13:30119400-30128600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr13:30119400-30128600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr13:30119400-30129200	Strong transcription	NHEK	skin
21	chr13:30119600-30128200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr13:30119600-30128600	Strong transcription	GM12878-XiMat	blood
23	chr13:30120000-30127000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr13:30120000-30128400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr13:30121000-30127200	Weak transcription	Brain Substantia Nigra	brain
26	chr13:30121000-30128600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr13:30121200-30128800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr13:30121200-30128800	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr13:30121400-30130000	Weak transcription	Adipose Nuclei	Adipose
30	chr13:30121800-30127800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr13:30121800-30128600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr13:30122000-30127800	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr13:30122000-30128200	Strong transcription	Hela-S3	cervix
34	chr13:30122200-30126000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr13:30122200-30127800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr13:30122200-30128000	Strong transcription	HSMMtube	muscle
37	chr13:30122200-30128200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr13:30122200-30128400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr13:30122200-30128600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr13:30122200-30128600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr13:30122200-30128800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr13:30122200-30128800	Strong transcription	Primary T cells from cord blood	blood
43	chr13:30122400-30126200	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr13:30122400-30126800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr13:30122400-30127800	Strong transcription	Fetal Thymus	thymus
46	chr13:30122400-30128000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr13:30122400-30128800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr13:30122600-30128000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr13:30122600-30128800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr13:30122600-30129000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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