Variant report

Variant	rs9849087
Chromosome Location	chr3:121465220-121465221
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:121463605..121466506-chr3:121466686..121468331,2	MCF-7	breast:
2	chr3:121442817..121449533-chr3:121463247..121470201,7	K562	blood:
3	chr3:121451393..121453533-chr3:121465182..121467129,2	K562	blood:
4	chr3:121462008..121465920-chr3:121468429..121472755,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173230	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11927625	0.81[CHB][hapmap]
rs12386356	0.98[EUR][1000 genomes]
rs16845505	1.00[CEU][hapmap]
rs34818685	0.87[AMR][1000 genomes]
rs59987610	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6770842	0.81[CHB][hapmap]
rs72626328	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7356043	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs9637385	0.94[ASN][1000 genomes]
rs9818194	0.81[CHB][hapmap]
rs9837315	0.88[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9841861	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	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9861782	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9863007	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[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];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	esv3399871	chr3:121465162-121467310	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers	Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
10	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers 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	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9849087	GOLGB1	cis	lymphoblastoid	seeQTL
rs9849087	IQCB1	cis	parietal	SCAN
rs9849087	GOLGB1	cis	multi-tissue	Pritchard
rs9849087	SLC15A2	cis	multi-tissue	Pritchard
rs9849087	SLC15A2	cis	parietal	SCAN
rs9849087	IQCB1	cis	cerebellum	SCAN

Chromatin state (count:103 , 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	chr3:121444600-121466400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:121444800-121466400	Weak transcription	Colonic Mucosa	Colon
5	chr3:121444800-121467200	Weak transcription	Aorta	Aorta
6	chr3:121444800-121467400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:121444800-121467400	Weak transcription	Spleen	Spleen
8	chr3:121445200-121466200	Weak transcription	Fetal Intestine Small	intestine
9	chr3:121445200-121466800	Weak transcription	Thymus	Thymus
10	chr3:121445200-121467400	Weak transcription	Esophagus	oesophagus
11	chr3:121445800-121467000	Weak transcription	Fetal Stomach	stomach
12	chr3:121445800-121467400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:121447600-121467000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:121447800-121466400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr3:121447800-121467000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:121448000-121466400	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:121448000-121466400	Weak transcription	Fetal Kidney	kidney
18	chr3:121448200-121466600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:121448400-121466400	Weak transcription	HSMM	muscle
20	chr3:121448400-121466800	Weak transcription	Hela-S3	cervix
21	chr3:121448600-121466400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:121448800-121465600	Weak transcription	HUVEC	blood vessel
23	chr3:121448800-121466400	Weak transcription	Fetal Lung	lung
24	chr3:121448800-121466400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:121448800-121466800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:121448800-121467400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr3:121448800-121467400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:121449000-121466400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:121449000-121466400	Weak transcription	HepG2	liver
30	chr3:121449000-121466800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:121449000-121467200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr3:121449000-121467200	Weak transcription	Fetal Thymus	thymus
33	chr3:121449600-121466400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:121449600-121466800	Weak transcription	Primary B cells from cord blood	blood
35	chr3:121449800-121467000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr3:121449800-121467200	Weak transcription	Placenta	Placenta
37	chr3:121450000-121466400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:121450000-121466400	Weak transcription	Fetal Intestine Large	intestine
39	chr3:121450000-121467000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr3:121450400-121466400	Weak transcription	HSMMtube	muscle
41	chr3:121450400-121466800	Weak transcription	Primary T cells from cord blood	blood
42	chr3:121450400-121467400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:121450600-121466400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:121450600-121466400	Weak transcription	Brain Substantia Nigra	brain
45	chr3:121451000-121466400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:121453800-121466400	Weak transcription	HMEC	breast
47	chr3:121454200-121466400	Weak transcription	NHDF-Ad	bronchial
48	chr3:121454200-121466800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:121454400-121466400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:121455000-121466800	Weak transcription	NHEK	skin

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