Variant report

Variant	rs1349402
Chromosome Location	chr7:129111305-129111306
allele	G/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:129010182..129012149-chr7:129109037..129111921,3	K562	blood:
2	chr7:128984621..128985408-chr7:129111176..129112056,2	K562	blood:
3	chr7:128858032..128859057-chr7:129111198..129112906,6	K562	blood:
4	chr7:129075089..129076920-chr7:129110497..129113086,2	K562	blood:
5	chr7:129102197..129105819-chr7:129107947..129111490,3	K562	blood:
6	chr7:129110547..129112326-chr7:129250138..129252974,2	K562	blood:
7	chr7:129007427..129007933-chr7:129110880..129111628,2	MCF-7	breast:
8	chr7:129013090..129015625-chr7:129110834..129113175,2	K562	blood:
9	chr7:129099938..129101762-chr7:129105861..129111774,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000273329	Chromatin interaction
ENSG00000106459	Chromatin interaction
ENSG00000158467	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11762085	1.00[CHB][hapmap];0.90[MKK][hapmap];1.00[ASN][1000 genomes]
rs11768409	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769581	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771549	1.00[JPT][hapmap]
rs11771705	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771841	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772187	0.89[ASN][1000 genomes]
rs13221695	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13221778	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13223151	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13241869	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13243857	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13247598	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1348750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349403	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1526897	0.89[ASN][1000 genomes]
rs1562291	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17552411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs17552570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs17552854	0.85[GIH][hapmap]
rs17553578	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628726	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2402952	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34275118	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34440172	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34911743	1.00[ASN][1000 genomes]
rs35084372	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35191983	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35294314	1.00[ASN][1000 genomes]
rs35312667	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35886223	0.89[ASN][1000 genomes]
rs36064596	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36086855	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62479481	1.00[ASN][1000 genomes]
rs62479487	1.00[ASN][1000 genomes]
rs62480621	0.89[ASN][1000 genomes]
rs62480623	0.89[ASN][1000 genomes]
rs62480628	0.89[ASN][1000 genomes]
rs62480631	0.89[ASN][1000 genomes]
rs62489087	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62489113	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62489119	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62489121	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs657664	1.00[CHD][hapmap]
rs68047560	1.00[ASN][1000 genomes]
rs6958637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs6971551	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6974105	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977752	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7781018	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7785864	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7805214	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428508	chr7:128946738-129114691	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv831128	chr7:129063040-129240800	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1349402	FAM40B	cis	cerebellum	SCAN
rs1349402	LOC407835	cis	cerebellum	SCAN
rs1349402	AHCYL2	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129080000-129128000	Weak transcription	HUVEC	blood vessel
2	chr7:129083800-129112800	Strong transcription	K562	blood
3	chr7:129093400-129134800	Weak transcription	Right Atrium	heart
4	chr7:129095200-129111800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:129095400-129115000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:129096800-129112000	Weak transcription	GM12878-XiMat	blood
7	chr7:129097600-129128600	Weak transcription	NH-A	brain
8	chr7:129100400-129113000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr7:129101600-129128600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:129102200-129124600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:129102400-129120400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:129103000-129117400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr7:129103000-129141200	Weak transcription	Hela-S3	cervix
14	chr7:129103200-129129600	Weak transcription	Dnd41	blood
15	chr7:129103200-129135400	Weak transcription	HepG2	liver
16	chr7:129104200-129141600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr7:129104800-129112000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr7:129104800-129121200	Weak transcription	Fetal Stomach	stomach
19	chr7:129105400-129127400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr7:129106600-129121400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:129107000-129121600	Weak transcription	Right Ventricle	heart
22	chr7:129107400-129124400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr7:129107600-129119800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr7:129108600-129111600	Weak transcription	NHDF-Ad	bronchial
25	chr7:129108800-129114400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr7:129108800-129115800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr7:129108800-129122400	Weak transcription	Left Ventricle	heart
28	chr7:129108800-129128600	Weak transcription	Osteobl	bone
29	chr7:129109000-129111400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:129109200-129125800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr7:129109600-129120400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr7:129109800-129120400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr7:129110400-129111600	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr7:129110400-129121400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr7:129110600-129115800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr7:129110800-129114800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr7:129110800-129115600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr7:129110800-129115800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr7:129110800-129119800	Weak transcription	Psoas Muscle	Psoas
40	chr7:129110800-129122600	Weak transcription	Brain Anterior Caudate	brain
41	chr7:129111000-129111600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr7:129111000-129111800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr7:129111000-129111800	Enhancers	HSMM	muscle
44	chr7:129111000-129112200	Enhancers	Muscle Satellite Cultured Cells	--
45	chr7:129111000-129112600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr7:129111000-129114800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr7:129111000-129120000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr7:129111200-129111400	Strong transcription	Fetal Heart	heart
49	chr7:129111200-129111800	Enhancers	HMEC	breast
50	chr7:129111200-129112000	Enhancers	NHEK	skin

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