Variant report

Variant	rs6901783
Chromosome Location	chr6:140098001-140098002
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:140091742..140094487-chr6:140097779..140099981,2	K562	blood:
2	chr6:140018170..140021108-chr6:140096378..140098271,2	MCF-7	breast:
3	chr6:140096649..140099517-chr6:140260643..140262599,2	K562	blood:
4	chr6:140081802..140083701-chr6:140096060..140098267,2	K562	blood:
5	chr6:140091742..140094049-chr6:140096525..140099279,2	K562	blood:
6	chr6:140093234..140095381-chr6:140096123..140098454,2	MCF-7	breast:
7	chr6:140096683..140098380-chr6:140468859..140470369,2	K562	blood:
8	chr6:139694049..139695787-chr6:140096448..140099243,2	K562	blood:
9	chr6:139930810..139933752-chr6:140097356..140098943,2	K562	blood:
10	chr6:139695846..139697718-chr6:140097081..140099970,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10499213	0.94[JPT][hapmap]
rs10499214	0.82[EUR][1000 genomes]
rs11962730	0.94[JPT][hapmap]
rs11964275	1.00[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs11965819	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12055436	0.81[JPT][hapmap]
rs12055472	0.81[JPT][hapmap]
rs12662206	0.94[JPT][hapmap]
rs12664473	0.87[JPT][hapmap]
rs17069206	0.81[JPT][hapmap]
rs17069225	0.81[JPT][hapmap]
rs17069373	0.83[ASN][1000 genomes]
rs1936214	0.81[EUR][1000 genomes]
rs2096283	0.94[JPT][hapmap]
rs2096284	0.94[JPT][hapmap]
rs2154032	1.00[CEU][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.81[EUR][1000 genomes]
rs4520026	0.82[EUR][1000 genomes]
rs4568471	0.83[ASN][1000 genomes]
rs4896488	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55966840	0.81[EUR][1000 genomes]
rs60052799	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6570374	0.94[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs6904036	0.83[ASN][1000 genomes]
rs6905478	0.94[CEU][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6911905	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6926194	0.85[ASN][1000 genomes]
rs6933318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933569	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73775693	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7743796	0.81[EUR][1000 genomes]
rs7752001	0.81[JPT][hapmap]
rs7756866	0.81[EUR][1000 genomes]
rs7769567	0.82[EUR][1000 genomes]
rs7772473	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7772713	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7774968	1.00[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs7776193	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9373246	0.81[JPT][hapmap]
rs9373247	0.94[JPT][hapmap]
rs9373248	0.93[JPT][hapmap]
rs9376452	0.81[JPT][hapmap]
rs9376463	0.98[ASN][1000 genomes]
rs9376464	0.89[ASN][1000 genomes]
rs9376466	0.85[ASN][1000 genomes]
rs9385874	1.00[CEU][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs9385875	0.82[EUR][1000 genomes]
rs9385876	0.94[JPT][hapmap]
rs9385879	0.84[ASN][1000 genomes]
rs9389717	0.83[CHD][hapmap];0.94[JPT][hapmap]
rs9389723	0.84[ASN][1000 genomes]
rs9399292	0.81[JPT][hapmap]
rs9399293	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9403114	0.81[EUR][1000 genomes]
rs9403115	1.00[CEU][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs9403116	0.93[JPT][hapmap]
rs9403124	0.82[ASN][1000 genomes]
rs9403125	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv830820	chr6:140059279-140255292	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6901783	MAP3K5	cis	parietal	SCAN
rs6901783	NHSL1	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140086000-140099400	Weak transcription	Ovary	ovary
2	chr6:140086000-140101000	Weak transcription	Left Ventricle	heart
3	chr6:140087400-140099200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:140087800-140098600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:140088200-140100000	Weak transcription	NHDF-Ad	bronchial
6	chr6:140096200-140100800	Enhancers	K562	blood
7	chr6:140096400-140099000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:140096400-140100200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr6:140096400-140100200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:140096400-140100400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:140096400-140100400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr6:140096400-140100800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:140096600-140100400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:140096800-140099000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:140096800-140099000	Enhancers	Stomach Smooth Muscle	stomach
16	chr6:140096800-140099600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr6:140097000-140098600	Enhancers	Fetal Lung	lung
18	chr6:140097000-140099600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr6:140097000-140099600	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr6:140097000-140100000	Enhancers	Fetal Heart	heart
21	chr6:140097000-140100200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr6:140097000-140100600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr6:140097000-140101000	Enhancers	Rectal Smooth Muscle	rectum
24	chr6:140097200-140098200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr6:140097200-140098600	Enhancers	Pancreas	Pancrea
26	chr6:140097200-140099200	Enhancers	Brain Germinal Matrix	brain
27	chr6:140097200-140099200	Enhancers	Colon Smooth Muscle	Colon
28	chr6:140097200-140099600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:140097200-140100200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:140097200-140100400	Enhancers	Fetal Brain Male	brain
31	chr6:140097400-140099400	Weak transcription	NHLF	lung
32	chr6:140097400-140099600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr6:140097400-140100600	Enhancers	Fetal Stomach	stomach
34	chr6:140097600-140098600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:140097600-140099000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:140097800-140098200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:140098000-140098800	Weak transcription	Fetal Kidney	kidney
38	chr6:140098000-140099000	Weak transcription	Fetal Muscle Leg	muscle
39	chr6:140098000-140099400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:140098000-140099400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:140098000-140099400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr6:140098000-140100800	Enhancers	Fetal Brain Female	brain

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