Variant report

Variant	rs12329244
Chromosome Location	chr2:114516494-114516495
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr2:114516132-114516501	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:114512582..114515674-chr2:114516372..114520568,3	MCF-7	breast:
2	chr2:114514472..114517401-chr2:114595773..114597784,2	MCF-7	breast:
3	chr2:114510034..114517579-chr2:114643441..114655407,23	MCF-7	breast:
4	chr2:114514479..114516685-chr2:114517501..114519701,2	K562	blood:
5	chr2:114511479..114519908-chr2:114641728..114650266,13	MCF-7	breast:
6	chr2:114489220..114494215-chr2:114513189..114517576,5	K562	blood:
7	chr2:114514673..114516598-chr2:114527693..114530348,3	K562	blood:

No data

Variant related genes	Relation type
SLC35F5	TF binding region
ENSG00000270019	Chromatin interaction
ENSG00000115091	Chromatin interaction
ENSG00000115084	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10169190	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197009	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199515	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208651	0.93[ASN][1000 genomes]
rs1062074	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11123202	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11123203	0.93[ASN][1000 genomes]
rs11677168	0.93[ASN][1000 genomes]
rs12711781	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12986781	0.86[ASN][1000 genomes]
rs13003858	0.86[ASN][1000 genomes]
rs13025042	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13028979	0.93[ASN][1000 genomes]
rs13389017	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13393247	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13395272	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13401587	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13407986	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13408264	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409879	0.84[EUR][1000 genomes]
rs13410586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416738	0.89[EUR][1000 genomes]
rs13417896	0.93[ASN][1000 genomes]
rs13424899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428433	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17048297	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17048299	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17048506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17633451	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs28392566	0.87[EUR][1000 genomes]
rs34026450	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34451679	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34480436	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35049717	0.86[EUR][1000 genomes]
rs35073956	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35255260	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap]
rs62158991	0.81[ASN][1000 genomes]
rs62170066	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6722177	0.87[ASN][1000 genomes]
rs7589738	1.00[CHB][hapmap]
rs7600251	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs998151	0.87[EUR][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	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv2883	chr2:114507889-114535199	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12329244	CHCHD5	cis	cerebellum	SCAN
rs12329244	SLC35F5	cis	cerebellum	SCAN
rs12329244	IL1B	cis	lymphoblastoid	seeQTL
rs12329244	SLC35F5	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114515200-114517600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr2:114515200-114517800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:114515200-114517800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:114515200-114517800	Weak transcription	NH-A	brain
5	chr2:114515200-114518200	Weak transcription	Psoas Muscle	Psoas
6	chr2:114515200-114519000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:114515200-114519600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:114515200-114519800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:114515200-114520400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:114515200-114520400	Weak transcription	Left Ventricle	heart
11	chr2:114515400-114517600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:114515400-114517600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:114515400-114517600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:114515400-114517600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:114515400-114517800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:114515400-114517800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:114515400-114517800	Weak transcription	HSMM	muscle
18	chr2:114515400-114517800	Weak transcription	HUVEC	blood vessel
19	chr2:114515400-114517800	Weak transcription	NHLF	lung
20	chr2:114515400-114517800	Weak transcription	Osteobl	bone
21	chr2:114515400-114518000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:114515400-114518000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:114515400-114519000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr2:114515400-114519000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr2:114515400-114519600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:114515400-114519800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:114515400-114519800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:114515400-114519800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:114515400-114519800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:114515400-114520000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:114515600-114519800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:114515600-114521600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:114516200-114517200	Enhancers	HSMMtube	muscle
34	chr2:114516400-114517000	Enhancers	NHDF-Ad	bronchial
35	chr2:114516400-114517200	Enhancers	GM12878-XiMat	blood

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