Variant report

Variant	rs7641330
Chromosome Location	chr3:142305638-142305639
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:142305398..142306280-chr3:142399277..142399935,3	MCF-7	breast:
2	chr3:142297092..142299718-chr3:142303138..142306954,3	MCF-7	breast:
3	chr3:142304116..142308988-chr3:142313771..142316581,4	MCF-7	breast:
4	chr3:142304999..142307775-chr3:142720336..142721986,2	MCF-7	breast:
5	chr3:142304087..142306838-chr3:142309222..142312026,2	K562	blood:
6	chr3:142305508..142306307-chr3:142712573..142713450,4	K562	blood:
7	chr3:106647215..106647782-chr3:142305386..142306279,2	MCF-7	breast:
8	chr3:142305364..142306466-chr3:142399184..142400223,7	MCF-7	breast:
9	chr3:142305390..142308830-chr3:142313114..142316758,5	MCF-7	breast:
10	chr3:142305389..142306193-chr3:142623757..142624589,2	K562	blood:
11	chr3:142296095..142299105-chr3:142305280..142307506,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000252745	Chromatin interaction
ENSG00000163714	Chromatin interaction
ENSG00000120756	Chromatin interaction
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10935465	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1129393	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11925693	0.93[CHD][hapmap];0.91[GIH][hapmap]
rs13061823	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap]
rs13065075	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13067795	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13069307	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13075471	0.85[EUR][1000 genomes]
rs13085998	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13093869	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13098343	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1357530	0.82[CEU][hapmap]
rs1983434	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs2030613	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs2049325	0.82[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap]
rs2140432	0.82[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap]
rs2227928	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2227930	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28617475	0.83[ASN][1000 genomes]
rs2862743	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap]
rs3922730	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4273389	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4413348	0.82[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap]
rs4441672	0.91[CHB][hapmap]
rs4597728	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6414350	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440082	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.81[TSI][hapmap]
rs6440086	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440087	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440088	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440089	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440090	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440091	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440092	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440093	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440094	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440098	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs6768093	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770155	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6772400	0.91[CHB][hapmap]
rs6775583	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6775718	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6775813	0.82[CEU][hapmap]
rs6780250	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6782400	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6791816	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6792259	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799752	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7428496	0.90[ASN][1000 genomes]
rs7610557	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7615316	0.82[CEU][hapmap]
rs7618253	0.80[LWK][hapmap];0.91[YRI][hapmap]
rs7623524	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7630130	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7631313	0.82[CEU][hapmap]
rs7634158	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7647573	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7651071	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7651542	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7652687	0.81[CEU][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap]
rs9683085	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9808914	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9808943	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9816736	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs9820353	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9820770	0.81[ASN][1000 genomes]
rs9825207	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826786	0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap]
rs9828178	0.81[ASN][1000 genomes]
rs9843148	0.87[CHB][hapmap]
rs9846960	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847364	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap]
rs9855140	0.82[ASN][1000 genomes]
rs9855919	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9862919	0.80[JPT][hapmap]
rs9866958	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs9869842	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9876254	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9879995	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[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	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7641330	XRN1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142298200-142314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:142298400-142306000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:142298600-142314400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:142305400-142305800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:142305400-142305800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:142305400-142306000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr3:142305400-142306200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:142305600-142305800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:142305600-142305800	Enhancers	Small Intestine	intestine
10	chr3:142305600-142306000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:142305600-142306000	Enhancers	NH-A	brain
12	chr3:142305600-142306200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:142305600-142306200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:142305600-142306200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:142305600-142306200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr3:142305600-142306200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:142305600-142306200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:142305600-142306200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:142305600-142306200	Enhancers	Liver	Liver
20	chr3:142305600-142306200	Enhancers	A549	lung
21	chr3:142305600-142306200	Enhancers	Hela-S3	cervix
22	chr3:142305600-142306200	Enhancers	HMEC	breast
23	chr3:142305600-142306200	Enhancers	HSMM	muscle
24	chr3:142305600-142306200	Enhancers	HSMMtube	muscle
25	chr3:142305600-142306200	Enhancers	NHDF-Ad	bronchial
26	chr3:142305600-142306200	Enhancers	NHEK	skin
27	chr3:142305600-142306200	Enhancers	Osteobl	bone
28	chr3:142305600-142306400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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