Variant report

Variant	rs6556884
Chromosome Location	chr5:95161340-95161341
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAL1	chr5:95161328-95161593	K562	blood:	n/a	n/a
2	MXI1	chr5:95161296-95161575	K562	blood:	n/a	n/a
3	MYC	chr5:95161308-95161661	K562	blood:	n/a	n/a
4	MAX	chr5:95161279-95161614	K562	blood:	n/a	n/a
5	BHLHE40	chr5:95161244-95161853	K562	blood:	n/a	n/a
6	GATA1	chr5:95161209-95161896	PBDE	blood:	n/a	chr5:95161497-95161504 chr5:95161496-95161506 chr5:95161494-95161504 chr5:95161495-95161507 chr5:95161497-95161506
7	JUND	chr5:95161266-95161636	K562	blood:	n/a	n/a
8	TEAD4	chr5:95161235-95161681	K562	blood:	n/a	n/a
9	POLR2A	chr5:95161296-95161479	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr5:95161300-95161659	K562	blood:	n/a	n/a
11	EGR1	chr5:95161301-95161511	K562	blood:	n/a	chr5:95161418-95161433
12	NR2F2	chr5:95161272-95161577	K562	blood:	n/a	n/a
13	RCOR1	chr5:95161207-95161701	K562	blood:	n/a	n/a
14	GATA1	chr5:95161055-95161935	K562	blood:	n/a	chr5:95161497-95161504 chr5:95161496-95161506 chr5:95161494-95161504 chr5:95161495-95161507 chr5:95161497-95161506
15	EP300	chr5:95161279-95161613	K562	blood:	n/a	chr5:95161421-95161434
16	GATA1	chr5:95161317-95161586	PBDEFetal	blood:	n/a	chr5:95161497-95161504 chr5:95161496-95161506 chr5:95161494-95161504 chr5:95161495-95161507 chr5:95161497-95161506

No.	Distal block	Cell Line	Cell type
1	chr5:95160713..95163370-chr5:95164070..95166105,2	MCF-7	breast:
2	chr5:95159650..95161680-chr5:95169175..95170926,2	MCF-7	breast:
3	chr5:95159839..95161506-chr5:95164819..95166390,2	MCF-7	breast:

Variant related genes	Relation type
GLRX	TF binding region
ENSG00000251000	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10059130	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10059138	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10059245	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10067881	1.00[ASN][1000 genomes]
rs10074815	0.94[ASN][1000 genomes]
rs10515230	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3756705	0.82[ASW][hapmap];0.92[LWK][hapmap];0.84[AFR][1000 genomes]
rs57148774	0.94[ASN][1000 genomes]
rs6556885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6556886	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs6556891	0.94[ASN][1000 genomes]
rs67807434	1.00[ASN][1000 genomes]
rs68044534	0.94[ASN][1000 genomes]
rs68095140	1.00[ASN][1000 genomes]
rs72785409	1.00[ASN][1000 genomes]
rs7700327	0.84[AFR][1000 genomes]

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	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv462255	chr5:95142817-95168155	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv598961	chr5:95142817-95168155	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv882389	chr5:95144952-95173887	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6556884	AC008592.3	cis	Whole Blood	GTEx
rs6556884	C5orf36	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95158800-95164800	Enhancers	Fetal Intestine Large	intestine
2	chr5:95159600-95161600	Weak transcription	Colon Smooth Muscle	Colon
3	chr5:95159800-95161400	Weak transcription	Brain Hippocampus Middle	brain
4	chr5:95159800-95162600	Enhancers	Liver	Liver
5	chr5:95159800-95164800	Enhancers	Fetal Intestine Small	intestine
6	chr5:95159800-95169800	Weak transcription	Fetal Kidney	kidney
7	chr5:95160000-95161800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
8	chr5:95160000-95161800	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr5:95160000-95162000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr5:95160000-95162000	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr5:95160200-95161600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:95160200-95161800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:95160200-95161800	Enhancers	Thymus	Thymus
14	chr5:95160200-95161800	Enhancers	HSMM	muscle
15	chr5:95160200-95162000	Enhancers	Duodenum Mucosa	Duodenum
16	chr5:95160200-95162200	Enhancers	Fetal Thymus	thymus
17	chr5:95160200-95164800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr5:95160200-95169800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:95160400-95161400	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr5:95160400-95161400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr5:95160400-95161600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr5:95160400-95161800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr5:95160400-95161800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr5:95160400-95161800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:95160400-95162000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr5:95160400-95162400	Enhancers	Primary T cells fromperipheralblood	blood
27	chr5:95160400-95162600	Enhancers	HepG2	liver
28	chr5:95160600-95161400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:95160600-95161800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr5:95160600-95162000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr5:95160600-95162000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr5:95160600-95162000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr5:95160600-95162000	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr5:95160600-95162200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr5:95160600-95162800	Weak transcription	Adipose Nuclei	Adipose
36	chr5:95160600-95162800	Weak transcription	Stomach Mucosa	stomach
37	chr5:95160600-95163200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr5:95160600-95163400	Weak transcription	Colonic Mucosa	Colon
39	chr5:95160600-95168800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr5:95160600-95170000	Weak transcription	Right Atrium	heart
41	chr5:95160600-95170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:95160800-95161600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr5:95160800-95161600	Weak transcription	Pancreas	Pancrea
44	chr5:95160800-95161600	Weak transcription	GM12878-XiMat	blood
45	chr5:95160800-95161800	Enhancers	Dnd41	blood
46	chr5:95160800-95162000	Enhancers	Primary T cells from cord blood	blood
47	chr5:95160800-95162000	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr5:95160800-95162000	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr5:95160800-95162400	Enhancers	Hela-S3	cervix
50	chr5:95160800-95162800	Weak transcription	Rectal Mucosa Donor 29	rectum

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