Variant report

Variant	rs6854776
Chromosome Location	chr4:7023479-7023480
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7021136..7024360-chr4:7026095..7028817,3	K562	blood:
2	chr4:6722979..6724789-chr4:7021205..7023795,2	MCF-7	breast:
3	chr4:6987057..6988717-chr4:7023046..7025909,2	K562	blood:
4	chr4:6987057..6989415-chr4:7022132..7024597,3	K562	blood:

Variant related genes	Relation type
ENSG00000132405	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10012590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516181	0.81[ASN][1000 genomes]
rs10937774	1.00[CHB][hapmap]
rs10937776	0.81[ASN][1000 genomes]
rs11732898	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs11938701	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11944897	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12502513	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs12503027	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510715	1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs13107989	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13108082	0.86[ASN][1000 genomes]
rs13111887	0.86[ASN][1000 genomes]
rs13122119	1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[ASN][1000 genomes]
rs13148395	1.00[ASN][1000 genomes]
rs13149411	0.93[ASN][1000 genomes]
rs13149923	0.86[ASN][1000 genomes]
rs2301817	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2301818	0.81[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[ASN][1000 genomes]
rs2301819	1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs2359194	0.81[ASN][1000 genomes]
rs3188939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34219101	0.86[ASN][1000 genomes]
rs34221933	1.00[ASN][1000 genomes]
rs34335938	0.93[ASN][1000 genomes]
rs34463709	0.93[ASN][1000 genomes]
rs34481892	0.93[ASN][1000 genomes]
rs34953654	0.81[ASN][1000 genomes]
rs34959511	0.93[ASN][1000 genomes]
rs35170004	0.93[ASN][1000 genomes]
rs35680216	0.86[ASN][1000 genomes]
rs3857171	0.81[ASN][1000 genomes]
rs3892490	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs3894945	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234788	0.86[ASN][1000 genomes]
rs4234791	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs4234793	0.87[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4544710	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4689059	1.00[CHD][hapmap]
rs4689560	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs4689563	0.93[ASN][1000 genomes]
rs4689564	0.93[ASN][1000 genomes]
rs4689565	0.93[ASN][1000 genomes]
rs4689566	0.81[ASN][1000 genomes]
rs4689567	0.81[ASN][1000 genomes]
rs4689568	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs4689573	0.81[ASN][1000 genomes]
rs4689575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689577	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4689578	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4689579	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55822670	0.86[ASN][1000 genomes]
rs62289166	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446559	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66530709	0.93[ASN][1000 genomes]
rs66640699	0.93[ASN][1000 genomes]
rs66841627	0.86[ASN][1000 genomes]
rs66931928	0.93[ASN][1000 genomes]
rs66992702	0.93[ASN][1000 genomes]
rs6811496	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816660	0.86[ASN][1000 genomes]
rs6816882	0.86[ASN][1000 genomes]
rs6818744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6831129	0.86[ASN][1000 genomes]
rs6834102	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839250	0.86[EUR][1000 genomes]
rs6840780	1.00[ASN][1000 genomes]
rs7655563	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7655773	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7658198	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7661462	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7661952	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7673901	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675524	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs7685667	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693321	0.81[ASN][1000 genomes]
rs8180337	0.85[CHD][hapmap]
rs9291126	0.83[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.86[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	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757919	chr4:6988148-7269901	Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv2759221	chr4:6988148-7269901	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv428436	chr4:6988148-7269901	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv593547	chr4:7002344-7032180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv469847	chr4:7003525-7168441	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv878531	chr4:7006541-7129556	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription 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	32 gene(s)	inside rSNPs	diseases
9	nsv878532	chr4:7010504-7055603	Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6854776	HMX1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6994000-7035600	Strong transcription	Fetal Stomach	stomach
2	chr4:6994000-7043200	Weak transcription	Right Atrium	heart
3	chr4:6994200-7035400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:6995800-7032800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:6996000-7035200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:6996400-7034800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:7000600-7034400	Strong transcription	Dnd41	blood
8	chr4:7001400-7034600	Strong transcription	Primary T cells from cord blood	blood
9	chr4:7001600-7035200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr4:7001600-7035400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr4:7001800-7029000	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr4:7001800-7035000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr4:7002000-7034400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr4:7002200-7035400	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr4:7002400-7034400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:7003600-7032600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:7008200-7034600	Strong transcription	Fetal Brain Female	brain
18	chr4:7008200-7035200	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr4:7008400-7035400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:7008400-7035400	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:7008800-7035000	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr4:7009800-7035200	Strong transcription	Fetal Intestine Large	intestine
23	chr4:7009800-7035600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr4:7010000-7034600	Strong transcription	Adipose Nuclei	Adipose
25	chr4:7010200-7024400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:7010200-7032600	Weak transcription	Stomach Mucosa	stomach
27	chr4:7010800-7035000	Strong transcription	Esophagus	oesophagus
28	chr4:7011200-7024400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:7011600-7036600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr4:7011600-7043600	Weak transcription	Psoas Muscle	Psoas
31	chr4:7013200-7044400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr4:7014200-7032800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr4:7014400-7034400	Strong transcription	Fetal Thymus	thymus
34	chr4:7014600-7028400	Strong transcription	Colonic Mucosa	Colon
35	chr4:7014600-7034600	Strong transcription	Thymus	Thymus
36	chr4:7014800-7029800	Strong transcription	Pancreas	Pancrea
37	chr4:7015400-7023600	Weak transcription	HSMM	muscle
38	chr4:7015400-7026800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr4:7016000-7031600	Weak transcription	HUVEC	blood vessel
40	chr4:7016400-7026600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr4:7016600-7029200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr4:7016600-7030200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr4:7016600-7034400	Strong transcription	Primary B cells from cord blood	blood
44	chr4:7016800-7032600	Strong transcription	Spleen	Spleen
45	chr4:7017400-7029000	Weak transcription	Fetal Brain Male	brain
46	chr4:7018000-7029000	Weak transcription	Fetal Kidney	kidney
47	chr4:7018400-7023800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:7018400-7043200	Weak transcription	Fetal Heart	heart
49	chr4:7018600-7031800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr4:7018600-7035600	Strong transcription	Fetal Intestine Small	intestine

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