Variant report

Variant	rs41377545
Chromosome Location	chr2:114519330-114519331
allele	A/C
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:6)
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	STAT3	chr2:114519259-114519428	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:114512582..114515674-chr2:114516372..114520568,3	MCF-7	breast:
2	chr2:114496162..114498041-chr2:114518174..114520618,2	K562	blood:
3	chr2:114512297..114513973-chr2:114517803..114519961,2	MCF-7	breast:
4	chr2:114514378..114516716-chr2:114517485..114519813,3	MCF-7	breast:
5	chr2:114511479..114519908-chr2:114641728..114650266,13	MCF-7	breast:
6	chr2:114514479..114516685-chr2:114517501..114519701,2	K562	blood:

No data

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

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10514810	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.97[ASN][1000 genomes]
rs11674510	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11676758	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11677881	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11679736	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11685171	0.84[ASN][1000 genomes]
rs11687572	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694541	1.00[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17632073	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17633527	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17683666	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17684620	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2166965	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.97[ASN][1000 genomes]
rs2290107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3748907	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4849271	0.95[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs58351064	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6708711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6709158	0.82[CHB][hapmap]
rs6725990	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6726001	0.82[CHB][hapmap]
rs6732182	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73955055	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs73955056	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs73955057	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs73955059	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73955070	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7581858	1.00[ASN][1000 genomes]
rs7599741	0.84[ASN][1000 genomes]
rs7599832	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9753198	0.84[AFR][1000 genomes];0.97[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	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs41377545	DDX11L2	cis	Whole Blood	GTEx
rs41377545	DDX11L2	cis	Nerve Tibial	GTEx
rs41377545	IL1A	cis	lymphoblastoid	seeQTL
rs41377545	RPL23AP7	Cis_1M	lymphoblastoid	RTeQTL
rs41377545	MERTK	cis	parietal	SCAN
rs41377545	RPL23AP7	cis	Whole Blood	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114515200-114519600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:114515200-114519800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:114515200-114520400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:114515200-114520400	Weak transcription	Left Ventricle	heart
5	chr2:114515400-114519600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:114515400-114519800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:114515400-114519800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:114515400-114519800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:114515400-114519800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:114515400-114520000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:114515600-114519800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:114515600-114521600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr2:114517400-114521000	Enhancers	NHDF-Ad	bronchial
14	chr2:114517600-114520200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr2:114517600-114520200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:114517600-114520400	Enhancers	HSMMtube	muscle
17	chr2:114517600-114521200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:114517800-114519800	Enhancers	Osteobl	bone
19	chr2:114517800-114520800	Enhancers	HSMM	muscle
20	chr2:114517800-114520800	Enhancers	HUVEC	blood vessel
21	chr2:114517800-114520800	Enhancers	NHLF	lung
22	chr2:114517800-114521200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:114518000-114519400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:114518000-114520800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:114518200-114519600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:114518400-114519800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:114519000-114519400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:114519000-114519400	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr2:114519200-114519600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:114519200-114519800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr2:114519200-114520000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:114519200-114520400	Weak transcription	Psoas Muscle	Psoas
33	chr2:114519200-114520800	Enhancers	NH-A	brain

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