Variant report

Variant	rs6490412
Chromosome Location	chr13:30143848-30143849
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:30139726..30141978-chr13:30142351..30145103,3	MCF-7	breast:
2	chr13:30140340..30147664-chr13:30167192..30171255,11	MCF-7	breast:
3	chr13:30137163..30140178-chr13:30141147..30143927,3	K562	blood:
4	chr13:30141734..30150637-chr13:30164575..30171336,12	MCF-7	breast:
5	chr13:30142186..30144552-chr13:30152474..30154361,2	MCF-7	breast:
6	chr13:30142867..30144693-chr13:30149445..30152081,2	MCF-7	breast:
7	chr13:30142261..30144231-chr13:30163491..30165148,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139514	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17073704	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1984029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1984030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2802247	0.85[CEU][hapmap]
rs280918	1.00[CHB][hapmap]
rs57340570	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59260312	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61508227	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6490411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7981502	1.00[CHB][hapmap]
rs866573	1.00[CHB][hapmap]
rs928352	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs928353	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

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:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30125000-30147400	Weak transcription	A549	lung
2	chr13:30126000-30161400	Weak transcription	Primary B cells from cord blood	blood
3	chr13:30126200-30147200	Weak transcription	Spleen	Spleen
4	chr13:30127600-30144000	Weak transcription	Fetal Intestine Small	intestine
5	chr13:30127600-30146200	Weak transcription	Right Ventricle	heart
6	chr13:30127600-30151400	Weak transcription	Aorta	Aorta
7	chr13:30127600-30156400	Weak transcription	Lung	lung
8	chr13:30127800-30147400	Weak transcription	Fetal Intestine Large	intestine
9	chr13:30127800-30147600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr13:30128000-30146800	Weak transcription	HSMMtube	muscle
11	chr13:30128000-30163600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr13:30128200-30146000	Weak transcription	Hela-S3	cervix
13	chr13:30128200-30147400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr13:30128200-30147400	Weak transcription	Thymus	Thymus
15	chr13:30128600-30146600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr13:30128600-30147400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr13:30128600-30161800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr13:30128800-30155800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr13:30128800-30168200	Weak transcription	Primary T cells from cord blood	blood
20	chr13:30131400-30147800	Weak transcription	Fetal Brain Female	brain
21	chr13:30131800-30147600	Weak transcription	GM12878-XiMat	blood
22	chr13:30136400-30146800	Weak transcription	NHLF	lung
23	chr13:30137200-30151000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr13:30137400-30147400	Weak transcription	Brain Angular Gyrus	brain
25	chr13:30137800-30147000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr13:30138000-30144200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr13:30138600-30147200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr13:30138600-30154000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr13:30138800-30146800	Weak transcription	Fetal Muscle Leg	muscle
30	chr13:30138800-30155800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr13:30138800-30159800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr13:30139000-30147000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr13:30139600-30144200	Weak transcription	Brain Substantia Nigra	brain
34	chr13:30139600-30147400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr13:30139800-30144000	Weak transcription	Brain Germinal Matrix	brain
36	chr13:30139800-30147200	Weak transcription	Osteobl	bone
37	chr13:30140000-30144000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr13:30140000-30144000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr13:30140000-30146000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr13:30140600-30149200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr13:30140800-30145000	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr13:30141000-30144400	Enhancers	HMEC	breast
43	chr13:30141000-30144800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr13:30141200-30147600	Weak transcription	Small Intestine	intestine
45	chr13:30141400-30144400	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr13:30141400-30144400	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr13:30141600-30144800	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr13:30141600-30145000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr13:30141600-30147000	Enhancers	H1 Cell Line	embryonic stem cell
50	chr13:30142200-30146800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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