Variant report

Variant	rs7001821
Chromosome Location	chr8:10129773-10129774
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	chr8:10118764..10122817-chr8:10126495..10130448,3	K562	blood:
2	chr8:9911202..9913645-chr8:10128676..10130785,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260093	Chromatin interaction
ENSG00000175806	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11774503	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs17151565	0.96[CEU][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6984840	0.89[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7013695	0.84[CEU][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes];0.80[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	nsv831230	chr8:9953343-10139350	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1021921	chr8:9958259-10212555	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv831231	chr8:10001214-10189094	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1026335	chr8:10037279-10139782	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1016347	chr8:10091475-10223667	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1028650	chr8:10101815-10178537	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7001821	TRPC4	trans	parietal	SCAN
rs7001821	BLK	cis	parietal	SCAN
rs7001821	SGCZ	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10123000-10138400	Weak transcription	Spleen	Spleen
2	chr8:10123600-10135400	Weak transcription	Fetal Intestine Small	intestine
3	chr8:10125600-10130600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr8:10125600-10136000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:10126200-10130000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr8:10126600-10132400	Enhancers	Fetal Brain Male	brain
7	chr8:10127600-10130400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr8:10128000-10129800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:10128200-10137000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr8:10128400-10130000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr8:10128400-10132200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr8:10128400-10133600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr8:10128400-10138200	Weak transcription	Fetal Brain Female	brain
14	chr8:10128600-10130000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr8:10129000-10133000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr8:10129000-10133200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr8:10129400-10130400	Enhancers	Liver	Liver
18	chr8:10129600-10130000	Weak transcription	Brain Germinal Matrix	brain
19	chr8:10129600-10130200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr8:10129600-10130800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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