Variant report

Variant	rs11900161
Chromosome Location	chr2:86427235-86427236
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr2:86426320-86427274	IMR90	lung:	n/a	n/a
2	TBP	chr2:86426352-86427299	Hela-S3	cervix:	n/a	n/a
3	TBP	chr2:86426326-86427355	K562	blood:	n/a	n/a
4	MXI1	chr2:86426426-86427239	Hela-S3	cervix:	n/a	n/a
5	TBL1XR1	chr2:86426417-86427680	K562	blood:	n/a	n/a
6	CHD1	chr2:86426317-86427692	IMR90	lung:	n/a	n/a
7	MXI1	chr2:86426148-86427499	SK-N-SH	brain:	n/a	n/a
8	EP300	chr2:86426319-86427344	ECC-1	luminal epithelium:	n/a	chr2:86426589-86426598 chr2:86426513-86426527
9	SIX5	chr2:86426220-86427249	A549	lung:	n/a	n/a
10	UBTF	chr2:86426439-86427274	K562	blood:	n/a	n/a
11	GATA3	chr2:86426251-86427238	A549	lung:	n/a	chr2:86426515-86426525
12	RELA	chr2:86426395-86427255	GM19099	blood:	n/a	n/a
13	POLR2A	chr2:86426313-86427247	Raji	blood:	n/a	n/a
14	JUN	chr2:86426416-86427246	K562	blood:	n/a	n/a
15	NR2F2	chr2:86426423-86427364	K562	blood:	n/a	n/a
16	IRF1	chr2:86427134-86427695	K562	blood:	n/a	n/a
17	IRF3	chr2:86426946-86427258	GM12878	blood:	n/a	n/a
18	UBTF	chr2:86426429-86427301	K562	blood:	n/a	n/a
19	MAX	chr2:86426370-86427306	HepG2	liver:	n/a	n/a
20	POLR2A	chr2:86426286-86427310	GM12891	blood:	n/a	n/a
21	MAX	chr2:86426412-86427292	Hela-S3	cervix:	n/a	n/a
22	MAX	chr2:86426320-86427242	K562	blood:	n/a	n/a
23	POLR2A	chr2:86426318-86427280	PBDE	blood:	n/a	n/a
24	EP300	chr2:86426379-86427621	GM12878	blood:	n/a	chr2:86426589-86426598 chr2:86426513-86426527
25	HCFC1	chr2:86426162-86427730	Hela-S3	cervix:	n/a	n/a
26	MAX	chr2:86426310-86427279	ECC-1	luminal epithelium:	n/a	n/a
27	NR2F2	chr2:86426089-86427257	K562	blood:	n/a	n/a
28	POLR2A	chr2:86426289-86427260	GM19099	blood:	n/a	n/a
29	ARID3A	chr2:86427208-86427783	K562	blood:	n/a	n/a
30	POLR2A	chr2:86426296-86427237	K562	blood:	n/a	n/a
31	POLR2A	chr2:86426407-86427255	K562	blood:	n/a	n/a
32	IRF1	chr2:86426309-86427746	K562	blood:	n/a	n/a
33	TCF12	chr2:86426039-86427298	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86420213..86424453-chr2:86424933..86430971,16	MCF-7	breast:

Variant related genes	Relation type
IMMT	TF binding region
ENSG00000273080	Chromatin interaction
ENSG00000265420	Chromatin interaction
ENSG00000132305	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10173155	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs10184462	0.83[CEU][hapmap]
rs10195199	0.85[CEU][hapmap]
rs10201457	0.90[MEX][hapmap]
rs11127016	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs12714175	0.85[CEU][hapmap]
rs12714177	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs13000103	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13001470	0.81[CEU][hapmap]
rs13007807	0.81[CEU][hapmap]
rs13027248	0.85[CEU][hapmap]
rs13403186	0.89[CEU][hapmap]
rs1540391	0.82[MEX][hapmap]
rs17584697	0.86[CHB][hapmap]
rs2059352	0.93[ASN][1000 genomes]
rs2194486	0.86[CHB][hapmap]
rs2241432	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs2288121	0.83[ASW][hapmap]
rs2288122	0.87[CHB][hapmap]
rs2303338	0.86[CHB][hapmap]
rs311576	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs311578	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs311579	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap]
rs3731818	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs3764949	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs3764950	0.81[CHB][hapmap]
rs3821017	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4832233	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs6547665	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs6707029	0.80[CEU][hapmap]
rs6725046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6731358	0.86[CHB][hapmap]
rs6735014	0.81[CEU][hapmap]
rs6740044	0.81[CEU][hapmap]
rs6740287	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6749090	0.89[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap]
rs6758173	0.82[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs717144	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs7422930	0.85[CEU][hapmap]
rs7560376	0.85[CEU][hapmap]
rs7563742	0.85[CEU][hapmap]
rs7567380	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7572386	0.81[CEU][hapmap]
rs7590445	0.88[CEU][hapmap]
rs9309633	0.81[CEU][hapmap]
rs9653508	0.89[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap]
rs965636	0.86[CHB][hapmap];0.87[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv1007474	chr2:86281967-86505453	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv997563	chr2:86281967-86506132	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv1008924	chr2:86282722-86499402	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv999956	chr2:86285944-86505453	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv1012768	chr2:86285944-86506132	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv1003207	chr2:86286314-86496732	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv1000441	chr2:86286314-86508168	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv535808	chr2:86286314-86508168	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv1004442	chr2:86286480-86506132	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv916616	chr2:86289130-86509326	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv458563	chr2:86292341-86507688	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv582370	chr2:86292341-86507688	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv1009140	chr2:86294939-86506132	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv582371	chr2:86296566-86507688	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv531381	chr2:86301091-86478346	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv1001157	chr2:86301440-86508168	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
19	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
20	nsv458574	chr2:86385728-86507688	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
21	nsv582372	chr2:86385728-86507688	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11900161	EDEM2	trans	cerebellum	SCAN
rs11900161	REEP1	cis	parietal	SCAN
rs11900161	MRPL35	cis	uninvolved skin	skin_eQTL
rs11900161	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs11900161	MRPL35	cis	parietal	SCAN
rs11900161	MRPL35	cis	brain	BrainEAC
rs11900161	IMMT	cis	multi-tissue	Pritchard
rs11900161	VPS24	cis	parietal	SCAN
rs11900161	IMMT	cis	lymphoblastoid	seeQTL
rs11900161	IMMT	cis	cerebellum	SCAN
rs11900161	IMMT	Cis_1M	lymphoblastoid	RTeQTL
rs11900161	IMMT	cis	Esophagus Muscularis	GTEx
rs11900161	IMMT	cis	Whole Blood	GTEx
rs11900161	MRPL35	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86425800-86427400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:86425800-86427400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:86425800-86427400	Active TSS	Stomach Smooth Muscle	stomach
4	chr2:86425800-86427800	Active TSS	NH-A	brain
5	chr2:86425800-86428200	Active TSS	A549	lung
6	chr2:86425800-86429800	Active TSS	GM12878-XiMat	blood
7	chr2:86426000-86427400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:86426000-86427400	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr2:86426000-86427400	Active TSS	Muscle Satellite Cultured Cells	--
10	chr2:86426000-86427400	Active TSS	Hela-S3	cervix
11	chr2:86426000-86427600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:86426000-86427600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:86426000-86427600	Active TSS	Fetal Intestine Large	intestine
14	chr2:86426000-86427600	Active TSS	Right Atrium	heart
15	chr2:86426000-86427600	Active TSS	Thymus	Thymus
16	chr2:86426000-86427600	Active TSS	HSMM	muscle
17	chr2:86426000-86427800	Active TSS	H1 Cell Line	embryonic stem cell
18	chr2:86426000-86427800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:86426000-86427800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:86426000-86427800	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr2:86426000-86427800	Active TSS	Brain Germinal Matrix	brain
22	chr2:86426000-86427800	Active TSS	Right Ventricle	heart
23	chr2:86426000-86428200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:86426000-86428400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:86426200-86427400	Active TSS	H9 Cell Line	embryonic stem cell
26	chr2:86426200-86427400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:86426200-86427400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:86426200-86427400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:86426200-86427400	Active TSS	Aorta	Aorta
30	chr2:86426200-86427400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:86426200-86427400	Active TSS	Fetal Intestine Small	intestine
32	chr2:86426200-86427400	Active TSS	Fetal Muscle Leg	muscle
33	chr2:86426200-86427400	Active TSS	Left Ventricle	heart
34	chr2:86426200-86427400	Active TSS	Ovary	ovary
35	chr2:86426200-86427400	Active TSS	HSMMtube	muscle
36	chr2:86426200-86427600	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr2:86426200-86427600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:86426200-86427600	Active TSS	Fetal Stomach	stomach
39	chr2:86426200-86427600	Active TSS	HMEC	breast
40	chr2:86426200-86427800	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr2:86426200-86427800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:86426200-86427800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:86426200-86427800	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr2:86426200-86427800	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr2:86426200-86427800	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr2:86426200-86427800	Active TSS	NHEK	skin
47	chr2:86426200-86428000	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr2:86426200-86428000	Active TSS	Psoas Muscle	Psoas
49	chr2:86426200-86428200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:86426200-86428200	Active TSS	NHLF	lung

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