Variant report

Variant	rs1269638
Chromosome Location	chr7:107885461-107885462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107885403..107887866-chr7:108208741..108211380,3	K562	blood:
2	chr7:107885138..107886888-chr7:108093240..108094894,2	K562	blood:
3	chr7:107844217..107846862-chr7:107884511..107886903,2	K562	blood:
4	chr7:107880432..107884512-chr7:107884667..107887859,3	MCF-7	breast:
5	chr7:107883815..107886718-chr7:108095136..108097625,2	MCF-7	breast:
6	chr7:107885444..107889446-chr7:107936320..107941216,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction
ENSG00000128590	Chromatin interaction
ENSG00000135241	Chromatin interaction
ENSG00000177683	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12111776	1.00[CHB][hapmap]
rs12111953	1.00[CHB][hapmap]
rs1269630	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1269631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269632	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269633	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269644	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1269646	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269647	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269654	1.00[CHB][hapmap];0.96[GIH][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs1269657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1544677	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17134753	1.00[CHB][hapmap]
rs17155059	1.00[CHB][hapmap]
rs17155074	1.00[CHB][hapmap]
rs17155081	1.00[CHB][hapmap]
rs17155094	1.00[CHB][hapmap]
rs17155125	1.00[CHB][hapmap]
rs382751	1.00[CHB][hapmap]
rs394921	1.00[CHB][hapmap]
rs399849	1.00[CHB][hapmap]
rs401573	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs420889	1.00[CHB][hapmap]
rs449919	1.00[CHB][hapmap]
rs4727701	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466219	1.00[CHB][hapmap]
rs6974903	1.00[CHB][hapmap]

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	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv949344	chr7:107396502-107987085	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1269638	LAMB4	cis	cerebellum	SCAN
rs1269638	RINT1	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107830400-107886400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr7:107860600-107886600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:107871200-107886400	Weak transcription	Brain Anterior Caudate	brain
4	chr7:107874800-107886200	Weak transcription	HSMMtube	muscle
5	chr7:107876400-107886400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:107877000-107885600	Weak transcription	HSMM	muscle
7	chr7:107877000-107886200	Weak transcription	HMEC	breast
8	chr7:107877800-107886400	Weak transcription	Pancreas	Pancrea
9	chr7:107880400-107886200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr7:107880600-107887000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr7:107880800-107886600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr7:107881000-107886200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:107881200-107886000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr7:107881200-107886400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr7:107881200-107886400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr7:107881200-107886400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:107881200-107886400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:107881200-107886600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr7:107881800-107886400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr7:107883600-107886800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:107884400-107886200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr7:107884400-107886200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:107884600-107886000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:107884600-107886200	Enhancers	NHDF-Ad	bronchial
25	chr7:107884800-107885600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr7:107884800-107885800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr7:107884800-107885800	Weak transcription	NHLF	lung
28	chr7:107884800-107886400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr7:107884800-107886400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr7:107884800-107886400	Weak transcription	Fetal Intestine Small	intestine
31	chr7:107884800-107890600	Weak transcription	Brain Substantia Nigra	brain
32	chr7:107885000-107886000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:107885200-107885600	Weak transcription	Osteobl	bone
34	chr7:107885200-107886400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr7:107885200-107886400	Enhancers	K562	blood
36	chr7:107885400-107885600	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr7:107885400-107885800	Transcr. at gene 5' and 3'	A549	lung
38	chr7:107885400-107886400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr7:107885400-107886400	Weak transcription	Fetal Intestine Large	intestine

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