Variant report

Variant	rs6461929
Chromosome Location	chr7:26371279-26371280
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	chr7:26369795..26371338-chr7:26373306..26375843,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12668538	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs12669686	0.82[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.85[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17153451	0.83[GIH][hapmap]
rs2391270	0.83[CHB][hapmap];0.89[YRI][hapmap]
rs2893246	0.87[GIH][hapmap];0.81[TSI][hapmap]
rs35911110	0.92[EUR][1000 genomes]
rs6950163	1.00[CEU][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021308	chr7:26116605-26419720	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv1018971	chr7:26161228-26380361	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv2761313	chr7:26340970-26389772	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6461929	SNX10	Cis_1M	lymphoblastoid	RTeQTL
rs6461929	C7orf46	cis	parietal	SCAN
rs6461929	SNX10	cis	lymphoblastoid	seeQTL
rs6461929	C7orf31	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26335200-26386400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr7:26345600-26386200	Weak transcription	Thymus	Thymus
3	chr7:26345800-26375600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr7:26346000-26373800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr7:26361000-26374000	Weak transcription	Fetal Thymus	thymus
6	chr7:26361800-26385400	Weak transcription	Pancreas	Pancrea
7	chr7:26367600-26378800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr7:26368600-26374600	Enhancers	Primary B cells from peripheral blood	blood
9	chr7:26368600-26377600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:26368800-26371400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr7:26368800-26374400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr7:26368800-26405000	Weak transcription	Placenta	Placenta
13	chr7:26369400-26379600	Weak transcription	HepG2	liver
14	chr7:26369800-26373400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr7:26370000-26371400	Weak transcription	Liver	Liver
16	chr7:26370200-26374000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr7:26370400-26372200	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr7:26370400-26374000	Enhancers	Primary B cells from cord blood	blood
19	chr7:26370400-26385000	Weak transcription	Spleen	Spleen
20	chr7:26370600-26371600	Weak transcription	GM12878-XiMat	blood
21	chr7:26370600-26372400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr7:26370600-26377400	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr7:26371200-26371800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr7:26371200-26373400	Weak transcription	Primary T cells from cord blood	blood
25	chr7:26371200-26374400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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