Variant report

Variant	rs4414209
Chromosome Location	chr11:3885511-3885512
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3885246..3886849-chr11:3888230..3890188,2	K562	blood:
2	chr11:3884366..3885941-chr11:3894780..3897079,2	K562	blood:

Variant related genes	Relation type
ENSG00000167323	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10160254	0.88[ASN][1000 genomes]
rs10160331	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10160415	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10160703	0.89[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10160753	0.88[ASN][1000 genomes]
rs10767679	0.92[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10767680	0.89[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10767681	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10767684	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10767685	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10835217	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835226	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10835231	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10835232	0.92[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10835236	0.95[CEU][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10835238	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10835239	0.95[CEU][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10835245	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10835246	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10835247	0.88[ASN][1000 genomes]
rs10835248	0.88[ASN][1000 genomes]
rs10835249	0.89[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10835250	0.88[ASN][1000 genomes]
rs10835252	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10835256	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10835261	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10835262	0.95[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10835270	0.82[MEX][hapmap];0.84[TSI][hapmap]
rs11030122	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11030128	0.80[ASN][1000 genomes]
rs11030176	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11030209	0.95[CEU][hapmap];0.89[JPT][hapmap]
rs11030211	0.82[MEX][hapmap];0.84[TSI][hapmap]
rs12275981	0.96[ASN][1000 genomes]
rs1869084	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap]
rs1869085	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4622250	0.95[CEU][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap]
rs4910582	0.85[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4910584	0.92[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7111609	0.95[CEU][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7113148	0.95[CEU][hapmap];0.90[JPT][hapmap]
rs7118295	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7120336	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7126252	0.81[ASN][1000 genomes]
rs7126870	0.83[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7131437	0.94[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7131469	0.88[ASN][1000 genomes]
rs7932404	0.85[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7952083	0.86[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking 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	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1046325	chr11:3856201-3895148	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv1039059	chr11:3856201-3909415	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
10	nsv540910	chr11:3856201-3909415	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1051580	chr11:3856201-3924216	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
12	nsv1043265	chr11:3856201-3926407	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
13	nsv896894	chr11:3859856-3888234	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
14	nsv869701	chr11:3879297-3973762	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4414209	RRM1	cis	Thyroid	GTEx
rs4414209	CD81	cis	parietal	SCAN
rs4414209	STIM1	cis	Thyroid	GTEx
rs4414209	IFITM3	cis	parietal	SCAN
rs4414209	HBE1	cis	cerebellum	SCAN
rs4414209	RRM1	cis	multi-tissue	Pritchard
rs4414209	TRIM21	cis	cerebellum	SCAN
rs4414209	OR51G2	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3878200-3886800	Weak transcription	NHLF	lung
2	chr11:3879400-3886600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr11:3879400-3887200	Weak transcription	Fetal Brain Female	brain
4	chr11:3880600-3886800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:3881000-3886000	Weak transcription	HMEC	breast
6	chr11:3881000-3886600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr11:3881000-3886800	Weak transcription	Brain Hippocampus Middle	brain
8	chr11:3881000-3888400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:3881200-3885600	Weak transcription	Lung	lung
10	chr11:3881200-3885800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:3881200-3886000	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr11:3881200-3886000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr11:3881200-3886000	Weak transcription	NHEK	skin
14	chr11:3881200-3886200	Weak transcription	NHDF-Ad	bronchial
15	chr11:3881200-3886400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:3881200-3886400	Weak transcription	HSMMtube	muscle
17	chr11:3881200-3886600	Weak transcription	Colonic Mucosa	Colon
18	chr11:3881200-3886600	Weak transcription	Placenta	Placenta
19	chr11:3881200-3886600	Weak transcription	Right Atrium	heart
20	chr11:3881200-3886600	Weak transcription	HSMM	muscle
21	chr11:3881200-3886800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr11:3881200-3886800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr11:3881200-3886800	Weak transcription	Brain Substantia Nigra	brain
24	chr11:3881200-3886800	Weak transcription	Esophagus	oesophagus
25	chr11:3881200-3886800	Weak transcription	Gastric	stomach
26	chr11:3881200-3886800	Weak transcription	Pancreas	Pancrea
27	chr11:3881200-3887000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr11:3881200-3887000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:3881200-3888400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr11:3881200-3888600	Weak transcription	Ovary	ovary
31	chr11:3881400-3885600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr11:3881400-3886000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:3882000-3886000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr11:3882000-3886600	Weak transcription	A549	lung
35	chr11:3882000-3886800	Weak transcription	NH-A	brain
36	chr11:3882200-3885600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:3882200-3885600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr11:3882200-3886400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr11:3882200-3888200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr11:3882400-3885800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr11:3882400-3886400	Weak transcription	Stomach Mucosa	stomach
42	chr11:3882400-3886600	Weak transcription	Brain Angular Gyrus	brain
43	chr11:3882400-3886600	Weak transcription	Osteobl	bone
44	chr11:3882400-3886800	Weak transcription	Fetal Stomach	stomach
45	chr11:3882400-3886800	Enhancers	K562	blood
46	chr11:3882400-3887000	Weak transcription	Brain Germinal Matrix	brain
47	chr11:3882600-3889400	Enhancers	Primary T cells fromperipheralblood	blood
48	chr11:3882800-3886800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:3882800-3888800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr11:3883000-3886200	Weak transcription	Rectal Mucosa Donor 31	rectum

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