Variant report

Variant	rs4656198
Chromosome Location	chr1:169826867-169826868
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:169826846-169827021	K562	blood:	n/a	n/a
2	POLR2A	chr1:169820501-169832002	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:169815223..169817412-chr1:169826417..169828144,2	K562	blood:
2	chr1:169825649..169828863-chr1:169858551..169863079,4	K562	blood:
3	chr1:169826425..169828479-chr1:169831022..169833757,2	K562	blood:
4	chr1:169823925..169827148-chr1:169828128..169831257,4	K562	blood:
5	chr1:169826041..169827646-chr1:169861241..169863079,2	K562	blood:
6	chr1:169816746..169819328-chr1:169826032..169828001,2	K562	blood:
7	chr1:169818930..169821400-chr1:169825229..169828152,2	K562	blood:

No data

Variant related genes	Relation type
RN7SL333P	TF binding region
ENSG00000000457	Chromatin interaction
ENSG00000239494	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10489175	0.94[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11577641	0.89[ASW][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.82[MEX][hapmap]
rs11578817	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11579102	0.89[ASW][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs11579709	0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11581959	0.94[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11585093	0.94[CHB][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11589659	0.93[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11589671	0.94[CHB][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs11590604	0.88[ASW][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs16828209	0.94[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs16862683	0.94[CHB][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs16862705	0.87[ASN][1000 genomes]
rs16862902	0.87[MKK][hapmap]
rs1928887	0.87[MKK][hapmap]
rs2420510	0.89[ASW][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2420511	0.89[ASW][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs34657513	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3766138	0.89[ASW][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3766139	0.94[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3766145	0.89[ASW][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3766146	0.94[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3766150	0.89[ASW][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.83[LWK][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3817859	0.94[CHB][hapmap];0.89[CHD][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs41496844	0.87[MKK][hapmap]
rs4656201	0.81[CHB][hapmap]
rs4656720	0.94[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4656722	0.94[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4656723	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4656726	0.89[ASW][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs4656732	0.87[MKK][hapmap]
rs55806711	0.86[ASN][1000 genomes]
rs57805301	0.85[ASN][1000 genomes]
rs58111285	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs60191157	0.85[ASN][1000 genomes]
rs60315765	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs61807812	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs61807813	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs61807814	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs61807817	0.85[ASN][1000 genomes]
rs61807818	0.81[ASN][1000 genomes]
rs61807835	0.86[ASN][1000 genomes]
rs6685211	0.94[CHB][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv872542	chr1:169802760-169844093	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4656198	SFT2D2	cis	cerebellum	SCAN
rs4656198	C1orf156	cis	lymphoblastoid	seeQTL
rs4656198	C1orf156	cis	parietal	SCAN
rs4656198	C1orf156	cis	cerebellum	SCAN
rs4656198	METTL18	cis	Artery Tibial	GTEx
rs4656198	METTL18	cis	Esophagus Muscularis	GTEx
rs4656198	ILDR2	cis	cerebellum	SCAN
rs4656198	KIFAP3	cis	cerebellum	SCAN
rs4656198	METTL18	cis	Esophagus Mucosa	GTEx
rs4656198	KIFAP3	cis	parietal	SCAN
rs4656198	KLHL11	trans	cerebellum	SCAN
rs4656198	METTL18	cis	lung	GTEx
rs4656198	C1orf156	Cis_1M	lymphoblastoid	RTeQTL
rs4656198	METTL18	cis	Adipose Subcutaneous	GTEx
rs4656198	METTL18	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169786600-169841400	Strong transcription	Dnd41	blood
3	chr1:169791200-169841200	Strong transcription	Fetal Thymus	thymus
4	chr1:169805400-169848800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
6	chr1:169808200-169841200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:169808600-169827000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:169809200-169829400	Strong transcription	GM12878-XiMat	blood
9	chr1:169809200-169829600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:169810000-169828000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:169810400-169841400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:169810600-169841200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr1:169810800-169841000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:169810800-169841200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:169811000-169841400	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr1:169811400-169827200	Strong transcription	K562	blood
17	chr1:169811600-169841200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:169811800-169827600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:169811800-169836200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:169811800-169841400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:169812000-169840800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:169812800-169836400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:169813400-169841200	Strong transcription	Fetal Intestine Large	intestine
24	chr1:169814200-169838000	Strong transcription	Placenta	Placenta
25	chr1:169814400-169830400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:169814400-169848600	Strong transcription	Duodenum Mucosa	Duodenum
27	chr1:169814600-169843200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:169814800-169836000	Strong transcription	Osteobl	bone
29	chr1:169814800-169848000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:169815000-169845200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr1:169815200-169843000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:169815200-169848200	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:169815400-169848400	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:169816600-169827800	Strong transcription	NHDF-Ad	bronchial
35	chr1:169817800-169829400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr1:169817800-169841000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:169817800-169848600	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr1:169818000-169832000	Strong transcription	Left Ventricle	heart
39	chr1:169818000-169838400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:169818000-169842800	Strong transcription	Primary B cells from cord blood	blood
41	chr1:169818200-169841200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:169818200-169847800	Strong transcription	Adipose Nuclei	Adipose
43	chr1:169819000-169848200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:169819400-169847000	Strong transcription	Liver	Liver
45	chr1:169820200-169832200	Strong transcription	Fetal Muscle Leg	muscle
46	chr1:169820200-169841400	Strong transcription	Fetal Muscle Trunk	muscle
47	chr1:169820400-169842600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:169820400-169844800	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:169820400-169847200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:169820600-169828600	Strong transcription	Muscle Satellite Cultured Cells	--

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