Variant report

Variant	rs11677881
Chromosome Location	chr2:114517864-114517865
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr2:114517696-114518566	SK-N-SH	brain:	n/a	n/a
2	NFIC	chr2:114517794-114518334	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr2:114517784-114518534	SK-N-SH	brain:	n/a	n/a
4	EP300	chr2:114517851-114518580	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr2:114517802-114518558	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr2:114517797-114518582	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr2:114517864-114518553	SK-N-SH	brain:	n/a	n/a
8	FOSL2	chr2:114517828-114518378	SK-N-SH	brain:	n/a	chr2:114518350-114518359
9	JUND	chr2:114517831-114518490	SK-N-SH	brain:	n/a	chr2:114518350-114518359
10	RXRA	chr2:114517840-114518413	SK-N-SH	brain:	n/a	n/a
11	TCF12	chr2:114517804-114518578	SK-N-SH	brain:	n/a	n/a
12	PBX3	chr2:114517860-114518446	SK-N-SH	brain:	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	chr2:114516554..114518950-chr2:114645999..114648586,2	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
ENSG00000115084	Chromatin interaction
ENSG00000115091	Chromatin interaction
ENSG00000270019	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10514810	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.92[ASN][1000 genomes]
rs11676758	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11679736	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11687572	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11694541	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17632073	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17633527	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17683666	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17684620	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166965	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.92[ASN][1000 genomes]
rs2290107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3748907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs41377545	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]
rs4849271	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs58351064	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6709158	0.82[CHB][hapmap]
rs6725990	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6726001	0.82[CHB][hapmap]
rs6732182	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73955055	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs73955056	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs73955057	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs73955059	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73955070	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581858	0.95[ASN][1000 genomes]
rs7599832	0.81[AFR][1000 genomes]
rs9753198	0.81[AFR][1000 genomes];0.92[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11677881	IL1A	cis	lymphoblastoid	seeQTL
rs11677881	MERTK	cis	parietal	SCAN
rs11677881	RPL23AP7	cis	multi-tissue	Pritchard
rs11677881	DDX11L2	cis	Whole Blood	GTEx
rs11677881	LOC644033	trans	multi-tissue	Pritchard
rs11677881	DDX11L2	cis	Nerve Tibial	GTEx
rs11677881	RPL23AP7	cis	Whole Blood	GTEx
rs11677881	MGC70863	trans	multi-tissue	Pritchard
rs11677881	MGC13005	trans	multi-tissue	Pritchard

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114515200-114518200	Weak transcription	Psoas Muscle	Psoas
2	chr2:114515200-114519000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:114515200-114519600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:114515200-114519800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:114515200-114520400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:114515200-114520400	Weak transcription	Left Ventricle	heart
7	chr2:114515400-114518000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:114515400-114518000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:114515400-114519000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:114515400-114519000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:114515400-114519600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:114515400-114519800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:114515400-114519800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:114515400-114519800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:114515400-114519800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:114515400-114520000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:114515600-114519800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:114515600-114521600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr2:114517400-114521000	Enhancers	NHDF-Ad	bronchial
20	chr2:114517600-114518000	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr2:114517600-114519200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:114517600-114520200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr2:114517600-114520200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:114517600-114520400	Enhancers	HSMMtube	muscle
25	chr2:114517600-114521200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:114517800-114518000	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr2:114517800-114518200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:114517800-114518200	Enhancers	Stomach Smooth Muscle	stomach
29	chr2:114517800-114518800	Enhancers	NH-A	brain
30	chr2:114517800-114519800	Enhancers	Osteobl	bone
31	chr2:114517800-114520800	Enhancers	HSMM	muscle
32	chr2:114517800-114520800	Enhancers	HUVEC	blood vessel
33	chr2:114517800-114520800	Enhancers	NHLF	lung
34	chr2:114517800-114521200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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