Variant report

Variant	rs4677663
Chromosome Location	chr3:194874605-194874606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194873006..194875023-chr3:194905477..194907059,2	K562	blood:
2	chr3:194865591..194868396-chr3:194874419..194877392,2	K562	blood:
3	chr3:194873057..194876086-chr3:194895720..194899560,4	K562	blood:
4	chr3:194840474..194843424-chr3:194874062..194876666,2	K562	blood:
5	chr3:194874240..194875817-chr3:194979341..194981767,2	K562	blood:

Variant related genes	Relation type
ENSG00000173950	Chromatin interaction
ENSG00000244314	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1009642	0.81[CEU][hapmap]
rs11721261	0.87[CEU][hapmap];0.90[CHB][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11917068	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1552893	0.95[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2131876	0.81[CEU][hapmap]
rs2172695	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2279630	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28573813	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3892194	0.81[CEU][hapmap]
rs4266129	0.86[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4300953	0.95[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4645095	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4677810	0.81[CEU][hapmap]
rs4677812	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4677818	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58370605	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60329099	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61218008	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6794540	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6797160	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs7612579	0.83[AMR][1000 genomes]
rs7639698	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7644208	0.81[CEU][hapmap]
rs7644678	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7646496	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs874198	0.81[CEU][hapmap]
rs903310	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs950257	0.95[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9848862	0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
11	nsv878137	chr3:194822098-194900432	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription 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	9 gene(s)	inside rSNPs	diseases
12	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
13	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
15	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
16	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
17	nsv1009120	chr3:194874494-194974672	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
19	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking 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	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4677663	RPL35A	cis	cerebellum	SCAN
rs4677663	C3orf21	cis	lymphoblastoid	seeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194861000-194881000	Weak transcription	Hela-S3	cervix
2	chr3:194861800-194875000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:194862400-194897800	Weak transcription	Dnd41	blood
4	chr3:194868200-194877800	Enhancers	Fetal Stomach	stomach
5	chr3:194868400-194877400	Enhancers	Fetal Heart	heart
6	chr3:194868800-194875000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:194868800-194885400	Enhancers	Fetal Muscle Leg	muscle
8	chr3:194869600-194876400	Enhancers	NHDF-Ad	bronchial
9	chr3:194869800-194876600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:194870800-194877600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:194871000-194877200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:194871000-194880800	Enhancers	HUVEC	blood vessel
13	chr3:194871400-194875800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:194871400-194877800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr3:194871400-194887400	Enhancers	Primary hematopoietic stem cells	blood
16	chr3:194871600-194875000	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr3:194871600-194875200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:194871600-194875800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:194871600-194876000	Enhancers	NHEK	skin
20	chr3:194871600-194877600	Enhancers	Fetal Intestine Large	intestine
21	chr3:194871600-194881200	Weak transcription	Liver	Liver
22	chr3:194871800-194874800	Enhancers	Rectal Smooth Muscle	rectum
23	chr3:194871800-194875000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:194871800-194875000	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:194871800-194875200	Enhancers	K562	blood
26	chr3:194871800-194875400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:194871800-194875600	Enhancers	NHLF	lung
28	chr3:194871800-194875800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:194871800-194876200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:194871800-194876400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr3:194871800-194876600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:194871800-194876800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:194871800-194876800	Enhancers	Osteobl	bone
34	chr3:194871800-194877000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr3:194871800-194878200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr3:194871800-194882800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:194872000-194875000	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr3:194872000-194875000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr3:194872000-194875200	Weak transcription	Thymus	Thymus
40	chr3:194872000-194875400	Weak transcription	Primary T cells from cord blood	blood
41	chr3:194872000-194875600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr3:194872000-194877000	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr3:194872000-194877200	Enhancers	Stomach Mucosa	stomach
44	chr3:194872000-194877400	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr3:194872000-194882800	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:194872000-194883000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:194872000-194883000	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr3:194872200-194875000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:194872200-194875200	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr3:194872200-194875200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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