Variant report

Variant	rs6804249
Chromosome Location	chr3:158439395-158439396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158438560..158442755-chr3:158443852..158445905,3	K562	blood:
2	chr3:158415825..158417591-chr3:158438376..158440279,2	MCF-7	breast:
3	chr3:158439350..158441066-chr3:158462153..158464983,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1006911	0.95[YRI][hapmap];0.80[ASN][1000 genomes]
rs1047366	0.92[ASW][hapmap];0.84[CEU][hapmap];0.81[YRI][hapmap]
rs12639052	0.82[CEU][hapmap];0.81[YRI][hapmap]
rs1346834	0.80[ASN][1000 genomes]
rs1435642	0.92[ASW][hapmap]
rs1656376	0.83[ASW][hapmap]
rs17699456	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1836688	0.92[ASW][hapmap];0.82[GIH][hapmap]
rs1864507	0.83[CEU][hapmap];0.81[YRI][hapmap]
rs1864508	0.80[ASN][1000 genomes]
rs2253249	0.90[YRI][hapmap]
rs2303909	0.92[ASW][hapmap];0.84[CEU][hapmap];0.80[GIH][hapmap];0.82[YRI][hapmap]
rs2364927	0.92[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2566346	0.99[ASN][1000 genomes]
rs3851362	0.83[CEU][hapmap]
rs4680460	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4875	0.92[ASW][hapmap];0.84[CEU][hapmap];0.84[GIH][hapmap]
rs57932243	0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs61794797	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441224	0.93[AFR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6772483	0.92[ASW][hapmap];0.84[CEU][hapmap];0.80[GIH][hapmap];0.82[YRI][hapmap]
rs6783879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6800914	0.83[CEU][hapmap]
rs6803047	0.84[CEU][hapmap]
rs6804259	0.80[YRI][hapmap]
rs7618110	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7621897	0.84[CEU][hapmap];0.82[YRI][hapmap]
rs7631310	0.92[ASW][hapmap];0.82[GIH][hapmap]
rs7635993	0.90[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs8455	0.84[CEU][hapmap];0.80[GIH][hapmap];0.82[YRI][hapmap]
rs891464	0.92[ASW][hapmap];0.84[CEU][hapmap];0.80[GIH][hapmap];0.82[YRI][hapmap]
rs9819567	0.84[CEU][hapmap];0.82[YRI][hapmap]
rs9822005	0.82[LWK][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap]
rs9825696	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9840571	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9861938	0.90[CHB][hapmap];0.81[CHD][hapmap];0.85[ASN][1000 genomes]
rs9863103	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[MKK][hapmap];0.90[YRI][hapmap];0.85[ASN][1000 genomes]
rs9866134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881462	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS 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 target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6804249	RARRES1	cis	cerebellum	SCAN
rs6804249	LXN	cis	parietal	SCAN
rs6804249	MLF1	cis	Heart Left Ventricle	GTEx
rs6804249	GFM1	cis	cerebellum	SCAN
rs6804249	LXN	cis	lymphoblastoid	seeQTL
rs6804249	TIPARP	cis	cerebellum	SCAN
rs6804249	GFM1	cis	parietal	SCAN
rs6804249	LXN	cis	cerebellum	SCAN
rs6804249	LXN	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158390800-158444200	Weak transcription	Gastric	stomach
2	chr3:158390800-158445400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:158397000-158443400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:158397000-158448000	Weak transcription	Thymus	Thymus
5	chr3:158399600-158445400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:158408400-158443000	Weak transcription	HepG2	liver
7	chr3:158411600-158439400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:158412200-158440800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:158415000-158440800	Weak transcription	Colonic Mucosa	Colon
10	chr3:158417600-158440600	Weak transcription	Aorta	Aorta
11	chr3:158424200-158446000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:158427600-158440600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:158427800-158440400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr3:158427800-158440600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr3:158427800-158440800	Weak transcription	Liver	Liver
16	chr3:158427800-158440800	Weak transcription	Esophagus	oesophagus
17	chr3:158429000-158440600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:158429600-158449000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:158429800-158440800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:158430600-158440800	Weak transcription	Small Intestine	intestine
21	chr3:158431000-158439600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:158431000-158439800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:158431000-158440600	Weak transcription	Fetal Thymus	thymus
24	chr3:158431000-158442000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:158431000-158442400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:158431000-158444200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:158431000-158445400	Weak transcription	GM12878-XiMat	blood
28	chr3:158431000-158449200	Weak transcription	Brain Germinal Matrix	brain
29	chr3:158431200-158445400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:158431200-158445800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:158431400-158439400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:158431400-158445400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:158431400-158445400	Weak transcription	Dnd41	blood
34	chr3:158432000-158445400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:158432000-158445400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:158432200-158439400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr3:158432200-158440600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:158432200-158444800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:158432200-158445400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:158432200-158445800	Weak transcription	Brain Substantia Nigra	brain
41	chr3:158432200-158449200	Weak transcription	Pancreas	Pancrea
42	chr3:158432400-158440600	Weak transcription	Lung	lung
43	chr3:158432400-158442600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:158433000-158439400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:158433200-158440600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr3:158433400-158440400	Weak transcription	Primary B cells from cord blood	blood
47	chr3:158433800-158440800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:158433800-158442800	Weak transcription	Spleen	Spleen
49	chr3:158434000-158440600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:158434000-158442600	Weak transcription	Stomach Smooth Muscle	stomach

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