Variant report

Variant	rs198676
Chromosome Location	chr6:143194288-143194289
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:143192752..143194574-chr6:143196705..143198471,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs107118	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs107119	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13211716	0.86[ASN][1000 genomes]
rs198669	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs198670	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs198671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198673	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs198674	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198679	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs198680	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2050311	0.85[ASN][1000 genomes]
rs28743065	0.83[ASN][1000 genomes]
rs4896599	0.89[ASN][1000 genomes]
rs5022324	0.81[ASN][1000 genomes]
rs67253362	0.85[ASN][1000 genomes]
rs6925325	0.86[ASN][1000 genomes]
rs8180684	0.87[ASN][1000 genomes]
rs9321878	0.81[ASN][1000 genomes]
rs9376710	0.89[ASN][1000 genomes]
rs9390025	0.89[ASN][1000 genomes]
rs9390026	0.87[ASN][1000 genomes]
rs9496470	0.83[ASN][1000 genomes]
rs9496471	0.83[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	nsv830829	chr6:143058408-143218077	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv538459	chr6:143165802-143360098	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143179600-143195000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:143179600-143195800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:143185600-143195000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:143185600-143195000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:143185600-143195000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:143185800-143195800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:143187000-143195800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:143188000-143195200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:143188600-143206200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:143189400-143197400	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr6:143189400-143198000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr6:143189400-143201400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:143189400-143205400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr6:143189400-143205800	Weak transcription	Fetal Stomach	stomach
15	chr6:143189600-143198400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr6:143189600-143204200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:143191200-143194400	Enhancers	Right Ventricle	heart
18	chr6:143191200-143196200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:143191200-143198800	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr6:143191200-143205600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr6:143191400-143194400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr6:143191600-143195800	Weak transcription	Placenta	Placenta
23	chr6:143191600-143199600	Weak transcription	Fetal Muscle Leg	muscle
24	chr6:143191800-143197800	Enhancers	Primary T cells from cord blood	blood
25	chr6:143192000-143194600	Enhancers	HMEC	breast
26	chr6:143192000-143195800	Weak transcription	Psoas Muscle	Psoas
27	chr6:143192200-143196400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:143192400-143194600	Enhancers	Fetal Intestine Small	intestine
29	chr6:143192400-143196000	Enhancers	Primary B cells from cord blood	blood
30	chr6:143192400-143196400	Enhancers	Primary B cells from peripheral blood	blood
31	chr6:143192800-143194400	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr6:143192800-143196800	Enhancers	Primary T cells fromperipheralblood	blood
33	chr6:143192800-143196800	Enhancers	Fetal Heart	heart
34	chr6:143193000-143194400	Enhancers	Left Ventricle	heart
35	chr6:143193000-143194400	Enhancers	Pancreas	Pancrea
36	chr6:143193000-143194400	Enhancers	Thymus	Thymus
37	chr6:143193000-143197800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:143193200-143195000	Weak transcription	Small Intestine	intestine
39	chr6:143193400-143194600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:143193400-143203800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr6:143193600-143194400	Enhancers	Brain Hippocampus Middle	brain
42	chr6:143193600-143194400	Enhancers	Ovary	ovary
43	chr6:143193600-143195000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr6:143193600-143195000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:143193600-143195800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:143193600-143196000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:143193600-143196200	Enhancers	HSMMtube	muscle
48	chr6:143193600-143196600	Enhancers	Fetal Intestine Large	intestine
49	chr6:143193600-143198600	Weak transcription	Brain Substantia Nigra	brain
50	chr6:143193600-143200800	Weak transcription	Fetal Thymus	thymus

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