Variant report

Variant	rs9841861
Chromosome Location	chr3:121453361-121453362
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:121452203..121455898-chr3:121466900..121469100,3	MCF-7	breast:
2	chr3:121448663..121450267-chr3:121453001..121454799,2	K562	blood:
3	chr3:121452246..121456088-chr3:121463734..121468790,6	MCF-7	breast:
4	chr3:121451393..121453533-chr3:121465182..121467129,2	K562	blood:

Variant related genes	Relation type
ENSG00000173230	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11927625	0.81[CHB][hapmap]
rs12386356	0.89[EUR][1000 genomes]
rs16845505	1.00[CEU][hapmap]
rs59987610	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6770842	0.81[CHB][hapmap]
rs72626328	0.84[AMR][1000 genomes]
rs7356043	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs9637385	0.95[ASN][1000 genomes]
rs9818194	0.81[CHB][hapmap]
rs9837315	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849087	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9859243	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs9859702	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9861782	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9863007	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9868875	0.81[CEU][hapmap]
rs9873644	0.81[CHB][hapmap]
rs9882312	1.00[CEU][hapmap]
rs9884018	1.00[CEU][hapmap];0.90[MEX][hapmap]
rs9968051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS 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 target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9841861	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs9841861	IQCB1	cis	parietal	SCAN
rs9841861	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs9841861	SLC15A2	cis	parietal	SCAN
rs9841861	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs9841861	GOLGB1	cis	lymphoblastoid	seeQTL
rs9841861	GOLGB1	cis	multi-tissue	Pritchard
rs9841861	IQCB1	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121436600-121466600	Weak transcription	Stomach Mucosa	stomach
2	chr3:121439400-121467200	Weak transcription	Small Intestine	intestine
3	chr3:121443400-121464800	Weak transcription	Fetal Brain Male	brain
4	chr3:121444600-121455200	Weak transcription	Psoas Muscle	Psoas
5	chr3:121444600-121466400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:121444800-121457200	Weak transcription	Gastric	stomach
7	chr3:121444800-121457200	Weak transcription	Right Ventricle	heart
8	chr3:121444800-121457400	Weak transcription	Pancreas	Pancrea
9	chr3:121444800-121458800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:121444800-121458800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:121444800-121466400	Weak transcription	Colonic Mucosa	Colon
12	chr3:121444800-121467200	Weak transcription	Aorta	Aorta
13	chr3:121444800-121467400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:121444800-121467400	Weak transcription	Spleen	Spleen
15	chr3:121445200-121457200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:121445200-121457800	Weak transcription	Lung	lung
17	chr3:121445200-121466200	Weak transcription	Fetal Intestine Small	intestine
18	chr3:121445200-121466800	Weak transcription	Thymus	Thymus
19	chr3:121445200-121467400	Weak transcription	Esophagus	oesophagus
20	chr3:121445800-121467000	Weak transcription	Fetal Stomach	stomach
21	chr3:121445800-121467400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:121447400-121456800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr3:121447600-121467000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:121447800-121466400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:121447800-121467000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:121448000-121453400	Weak transcription	A549	lung
27	chr3:121448000-121453800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:121448000-121457800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:121448000-121466400	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:121448000-121466400	Weak transcription	Fetal Kidney	kidney
31	chr3:121448200-121458400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:121448200-121458800	Weak transcription	Dnd41	blood
33	chr3:121448200-121466600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:121448400-121466400	Weak transcription	HSMM	muscle
35	chr3:121448400-121466800	Weak transcription	Hela-S3	cervix
36	chr3:121448600-121458800	Weak transcription	Adipose Nuclei	Adipose
37	chr3:121448600-121466400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:121448800-121453400	Weak transcription	NHLF	lung
39	chr3:121448800-121453600	Weak transcription	NH-A	brain
40	chr3:121448800-121453600	Weak transcription	NHDF-Ad	bronchial
41	chr3:121448800-121453800	Weak transcription	Osteobl	bone
42	chr3:121448800-121455200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:121448800-121457400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:121448800-121457800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:121448800-121458800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:121448800-121459200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:121448800-121460000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:121448800-121460400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:121448800-121463600	Weak transcription	Ovary	ovary
50	chr3:121448800-121464600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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