Variant report

Variant	rs6674490
Chromosome Location	chr1:185136458-185136459
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:185135577..185140535-chr1:185283801..185287464,5	K562	blood:
2	chr1:185118825..185122081-chr1:185134391..185138048,3	K562	blood:
3	chr1:185135724..185140535-chr1:185281992..185285991,5	K562	blood:
4	chr1:185133181..185136561-chr1:185138198..185141782,4	K562	blood:

Variant related genes	Relation type
ENSG00000116679	Chromatin interaction
ENSG00000231084	Chromatin interaction
ENSG00000273004	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1008502	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs10453829	0.84[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs10489579	0.84[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10489581	0.84[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap]
rs1053166	0.84[TSI][hapmap]
rs10737256	0.90[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10797999	0.90[ASW][hapmap];1.00[CEU][hapmap];0.89[MKK][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10911674	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs10911678	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10911679	0.84[TSI][hapmap]
rs10911680	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11588646	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12022419	0.84[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap]
rs12025737	0.86[AMR][1000 genomes]
rs12035073	0.84[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs12037692	0.84[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs12038919	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs12043427	0.84[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap]
rs12043495	0.84[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs12043617	0.84[CHB][hapmap]
rs12046095	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs12081098	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12408279	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs12409926	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs1322646	0.90[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1407554	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs1407556	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1407557	0.91[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1415072	0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs1884447	0.81[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2050566	0.84[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs2057222	0.81[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes]
rs2146328	0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs2146329	0.90[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2378958	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs28609768	0.81[TSI][hapmap]
rs3753569	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3766720	0.84[CHB][hapmap]
rs3766723	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs4549995	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57188163	0.84[ASN][1000 genomes]
rs6684586	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs6698122	0.80[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs6700484	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7519019	0.83[ASW][hapmap];0.81[GIH][hapmap]
rs7523448	0.86[TSI][hapmap]
rs7547420	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7548237	0.86[TSI][hapmap]
rs950327	0.81[GIH][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers 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	69 gene(s)	inside rSNPs	diseases
3	nsv548396	chr1:185038104-185151378	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv521613	chr1:185071831-185171869	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6674490	RNF2	cis	Liver	GTEx
rs6674490	QSOX1	cis	cerebellum	SCAN
rs6674490	KRT84	trans	multi-tissue	Pritchard
rs6674490	KRT84	cis	Liver	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185127200-185147000	Weak transcription	Spleen	Spleen
2	chr1:185127200-185169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:185127400-185144400	Weak transcription	Pancreas	Pancrea
4	chr1:185127400-185152200	Weak transcription	Aorta	Aorta
5	chr1:185127400-185153000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:185127400-185157400	Weak transcription	Small Intestine	intestine
7	chr1:185127400-185163400	Weak transcription	Esophagus	oesophagus
8	chr1:185127400-185192000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:185127600-185138400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:185127600-185138800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:185127600-185139200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:185127600-185139400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:185127600-185139400	Weak transcription	Fetal Kidney	kidney
14	chr1:185127600-185144400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:185127600-185144800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr1:185127600-185145200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:185127600-185145400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:185127600-185147400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:185127600-185170000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:185127600-185184600	Weak transcription	Psoas Muscle	Psoas
21	chr1:185127600-185218200	Weak transcription	Right Ventricle	heart
22	chr1:185127800-185147000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:185128000-185136600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:185128000-185137000	Weak transcription	NH-A	brain
25	chr1:185128000-185166400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:185128200-185139400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:185128200-185139400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:185128200-185139400	Weak transcription	Dnd41	blood
29	chr1:185128200-185147200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:185128200-185153800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:185128200-185161200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:185128400-185137000	Weak transcription	Stomach Mucosa	stomach
33	chr1:185128400-185139400	Weak transcription	Hela-S3	cervix
34	chr1:185128400-185139600	Weak transcription	NHLF	lung
35	chr1:185128400-185145400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr1:185128400-185155200	Weak transcription	NHDF-Ad	bronchial
37	chr1:185128400-185193800	Weak transcription	Brain Angular Gyrus	brain
38	chr1:185128400-185201800	Weak transcription	Gastric	stomach
39	chr1:185128600-185168200	Weak transcription	Fetal Heart	heart
40	chr1:185128600-185171400	Weak transcription	Fetal Brain Male	brain
41	chr1:185129200-185139200	Weak transcription	K562	blood
42	chr1:185129600-185138200	Weak transcription	HSMM	muscle
43	chr1:185130000-185137400	Strong transcription	Fetal Brain Female	brain
44	chr1:185130200-185137400	Strong transcription	Brain Germinal Matrix	brain
45	chr1:185130200-185138000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:185130400-185137800	Strong transcription	Adipose Nuclei	Adipose
47	chr1:185130600-185137200	Strong transcription	Primary T cells from cord blood	blood
48	chr1:185130800-185139400	Weak transcription	Fetal Thymus	thymus
49	chr1:185130800-185139400	Weak transcription	GM12878-XiMat	blood
50	chr1:185131600-185173000	Weak transcription	Brain Substantia Nigra	brain

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