Variant report

Variant	rs12200371
Chromosome Location	chr6:38446634-38446635
allele	A/G
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	POLR2A	chr6:38446617-38446687	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38443341..38445345-chr6:38445490..38448475,2	MCF-7	breast:
2	chr6:38441969..38444159-chr6:38445659..38447643,2	K562	blood:

Variant related genes	Relation type
BTBD9-AS1	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12528414	0.91[JPT][hapmap]
rs12528646	0.92[JPT][hapmap]
rs12528840	0.92[JPT][hapmap]
rs12662621	0.83[CEU][hapmap]
rs13199426	0.92[CEU][hapmap]
rs16890715	0.92[JPT][hapmap]
rs16890751	0.88[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs28889620	0.81[AFR][1000 genomes]
rs35978718	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4236059	1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs4316001	0.88[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4454130	1.00[JPT][hapmap];0.89[YRI][hapmap]
rs59594955	1.00[ASN][1000 genomes]
rs60581943	0.98[ASN][1000 genomes]
rs61088409	0.86[ASN][1000 genomes]
rs6900510	0.92[CEU][hapmap]
rs6912811	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6914430	0.92[JPT][hapmap]
rs7764900	0.82[JPT][hapmap]
rs9462435	1.00[CEU][hapmap]
rs9470878	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs9470879	0.87[ASW][hapmap];0.92[CEU][hapmap];0.83[TSI][hapmap]
rs9470884	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap]
rs9470887	1.00[CEU][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs9470889	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9688895	0.92[ASN][1000 genomes]
rs9689697	0.98[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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv602958	chr6:38362024-38446634	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1030889	chr6:38374812-38450432	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38396400-38449800	Weak transcription	Primary B cells from cord blood	blood
2	chr6:38437000-38455400	Weak transcription	Gastric	stomach
3	chr6:38440200-38449800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr6:38443400-38447400	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr6:38444200-38446800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr6:38444200-38447000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr6:38444400-38447200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:38444600-38447400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr6:38444600-38496200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:38444800-38447000	Enhancers	H9 Cell Line	embryonic stem cell
11	chr6:38444800-38447200	Enhancers	H1 Cell Line	embryonic stem cell
12	chr6:38444800-38449800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:38445000-38448600	Weak transcription	Fetal Brain Female	brain
14	chr6:38445400-38452600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:38445600-38448600	Weak transcription	Brain Germinal Matrix	brain
16	chr6:38445600-38448600	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr6:38445800-38446800	Weak transcription	Right Atrium	heart
18	chr6:38445800-38447000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:38446000-38448400	Weak transcription	Fetal Brain Male	brain
20	chr6:38446000-38449200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:38446200-38447000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr6:38446200-38447200	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr6:38446200-38453400	Weak transcription	Primary T cells from cord blood	blood
24	chr6:38446400-38447600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr6:38446600-38446800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr6:38446600-38447200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
27	chr6:38446600-38455400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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