Variant report

Variant	rs6855349
Chromosome Location	chr4:73956736-73956737
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:73933270..73937435-chr4:73951806..73956977,6	K562	blood:
2	chr4:73955525..73957115-chr4:73962530..73964538,2	K562	blood:
3	chr4:73956326..73957952-chr4:73959384..73961051,2	K562	blood:
4	chr4:73955114..73957841-chr4:73972791..73974834,2	K562	blood:
5	chr4:73955980..73958967-chr4:74123435..74128733,4	K562	blood:
6	chr4:73946540..73955069-chr4:73955536..73964230,11	K562	blood:
7	chr4:73950560..73953123-chr4:73954043..73956858,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132466	Chromatin interaction
ENSG00000163626	Chromatin interaction
ENSG00000250220	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1052080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11721329	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11727957	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11929937	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11939939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12500051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12507846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13107336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13135799	0.81[ASN][1000 genomes]
rs13149759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13151642	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17178078	0.82[ASN][1000 genomes]
rs1996057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs34230856	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34716955	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3762883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56261590	0.84[EUR][1000 genomes]
rs62309635	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67424539	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7442235	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs973541	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949371	chr4:73678470-74094500	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv432611	chr4:73740665-74099265	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv523169	chr4:73752242-74120910	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv998707	chr4:73753922-74044843	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers 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 target site	18 gene(s)	inside rSNPs	diseases
5	nsv537136	chr4:73753922-74044843	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv917017	chr4:73754127-74044830	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	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv1013174	chr4:73785324-74031884	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv537137	chr4:73785324-74031884	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1012068	chr4:73817769-74003079	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv1014088	chr4:73817769-74031884	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv537138	chr4:73817769-74031884	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv533502	chr4:73819067-74044813	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	esv1849323	chr4:73926670-74115116	Strong transcription Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6855349	AFM	cis	parietal	SCAN
rs6855349	COX18	cis	parietal	SCAN
rs6855349	EREG	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:73936000-73956800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:73936000-73969600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:73936200-73980000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:73936400-73970000	Weak transcription	Stomach Mucosa	stomach
5	chr4:73938800-74005200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:73939000-73969600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:73939000-74005000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:73939400-73970000	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:73940400-74043400	Strong transcription	Fetal Thymus	thymus
10	chr4:73942800-73956800	Weak transcription	Colonic Mucosa	Colon
11	chr4:73943200-73957000	Weak transcription	Psoas Muscle	Psoas
12	chr4:73946800-73968000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:73949200-73988200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:73950600-74004200	Strong transcription	HSMM	muscle
15	chr4:73951000-73958200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:73952200-73957000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:73952400-73957000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr4:73952400-73957200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr4:73952800-73992400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:73952800-74023000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:73953000-73969800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:73953600-73963400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr4:73954600-73968400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr4:73954600-73992200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:73954600-73995400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:73954800-73957800	Strong transcription	Fetal Intestine Small	intestine
27	chr4:73954800-73957800	Strong transcription	Fetal Stomach	stomach
28	chr4:73954800-73958000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:73955000-73960600	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr4:73955000-73963200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:73955200-73962000	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr4:73955200-73972800	Strong transcription	Placenta	Placenta
33	chr4:73955200-73991400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:73955200-73991600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:73955400-73970400	Strong transcription	Dnd41	blood
36	chr4:73955600-73958800	Strong transcription	Fetal Intestine Large	intestine
37	chr4:73955600-73968200	Strong transcription	Osteobl	bone
38	chr4:73955800-73957800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:73955800-73958000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:73955800-73958000	Strong transcription	Primary hematopoietic stem cells	blood
41	chr4:73955800-73958000	Strong transcription	Fetal Lung	lung
42	chr4:73955800-73958000	Strong transcription	Lung	lung
43	chr4:73955800-73958000	Strong transcription	Ovary	ovary
44	chr4:73955800-73958000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:73955800-73958000	Strong transcription	Thymus	Thymus
46	chr4:73955800-73958200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:73955800-73958200	Strong transcription	Adipose Nuclei	Adipose
48	chr4:73955800-73958400	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr4:73955800-73958800	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr4:73955800-73968600	Strong transcription	HUES6 Cell Line	embryonic stem cell

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