Variant report

Variant	rs6795197
Chromosome Location	chr3:141047072-141047073
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141027128..141029187-chr3:141047055..141049499,2	MCF-7	breast:
2	chr3:141046937..141049134-chr3:141051333..141055060,4	K562	blood:
3	chr3:141044888..141047671-chr3:141061362..141063749,2	K562	blood:
4	chr3:141044600..141047576-chr3:141085948..141088845,2	MCF-7	breast:
5	chr3:141044721..141047194-chr3:141049083..141050797,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249417	Chromatin interaction
ENSG00000177311	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1511380	0.87[ASW][hapmap];1.00[CHD][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs17787621	1.00[ASN][1000 genomes]
rs1983235	0.96[CEU][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4132036	1.00[ASN][1000 genomes]
rs4325905	0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs56054141	1.00[ASN][1000 genomes]
rs59539710	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6765857	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6771916	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6777886	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795377	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616781	0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs7636469	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829470	0.91[YRI][hapmap]
rs9843461	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv460871	chr3:141027614-141074962	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv591893	chr3:141027614-141074962	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6795197	RASA2	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141031800-141047400	Weak transcription	Right Ventricle	heart
2	chr3:141040600-141049000	Weak transcription	Hela-S3	cervix
3	chr3:141040600-141049200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:141045200-141047600	Weak transcription	NHDF-Ad	bronchial
5	chr3:141045800-141047800	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr3:141045800-141049000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:141045800-141049200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:141045800-141050000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:141045800-141050200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:141045800-141051200	Weak transcription	Lung	lung
11	chr3:141046000-141053800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:141046200-141047800	Enhancers	Duodenum Mucosa	Duodenum
13	chr3:141046200-141049000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:141046200-141049400	Weak transcription	HUVEC	blood vessel
15	chr3:141046200-141053400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:141046200-141055800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:141046400-141047400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:141046400-141049000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:141046400-141049000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:141046400-141049800	Weak transcription	HepG2	liver
21	chr3:141046400-141052400	Weak transcription	Pancreas	Pancrea
22	chr3:141046400-141055800	Genic enhancers	Fetal Intestine Small	intestine
23	chr3:141046600-141047400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr3:141046600-141048400	Enhancers	K562	blood
25	chr3:141046800-141047800	Enhancers	Colonic Mucosa	Colon
26	chr3:141047000-141047200	Flanking Active TSS	GM12878-XiMat	blood
27	chr3:141047000-141047600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:141047000-141047800	Enhancers	Fetal Heart	heart
29	chr3:141047000-141047800	Enhancers	Small Intestine	intestine
30	chr3:141047000-141047800	Enhancers	A549	lung
31	chr3:141047000-141055800	Genic enhancers	Fetal Intestine Large	intestine

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