Variant report

Variant	rs7749600
Chromosome Location	chr6:86334090-86334091
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:86323280..86334231-chr6:86380512..86390230,24	K562	blood:
2	chr6:86333946..86338132-chr6:86385754..86388640,4	MCF-7	breast:
3	chr6:86316554..86318290-chr6:86332242..86335078,2	MCF-7	breast:
4	chr6:86332640..86335317-chr6:86382915..86385234,3	K562	blood:
5	chr6:86332635..86335527-chr6:86336788..86338343,3	K562	blood:

Variant related genes	Relation type
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs12055597	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12524836	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12528808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12662033	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12664908	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1570311	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1590279	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2229524	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3812137	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[MKK][hapmap];0.81[ASN][1000 genomes]
rs3812139	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4144167	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4327657	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4373339	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap]
rs4400191	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap]
rs4458647	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4487548	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4565270	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs59744370	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6900270	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6902638	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]
rs6902904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6906618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6910543	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6913634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6923017	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930543	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6930790	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs6942065	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs73751215	0.81[ASN][1000 genomes]
rs7744309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7745560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7752105	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7753022	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7760309	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7766284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7771187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7771366	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7775016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap]
rs7775788	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9344528	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs9344530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9344538	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9351063	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9351066	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9353319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9353321	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9353323	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9353324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9359655	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9359656	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9362223	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9362225	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9362226	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444353	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444356	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450278	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9450280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9450286	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.81[ASN][1000 genomes]
rs9450289	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450294	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450295	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450299	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9450300	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450304	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450307	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]
rs9450308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450309	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][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	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
4	esv1792638	chr6:86224053-86336300	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS 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	15 gene(s)	inside rSNPs	diseases
5	nsv5383	chr6:86303223-86348023	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7749600	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs7749600	NT5E	cis	lymphoblastoid	seeQTL
rs7749600	NT5E	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86305800-86336200	Weak transcription	Fetal Heart	heart
2	chr6:86313400-86349000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr6:86313600-86338400	Strong transcription	GM12878-XiMat	blood
4	chr6:86313800-86340200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:86314200-86338200	Strong transcription	Dnd41	blood
6	chr6:86314200-86341200	Strong transcription	HMEC	breast
7	chr6:86314600-86334600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:86314800-86348600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:86315000-86347800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:86315200-86338200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:86315400-86338200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:86315400-86338200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:86315400-86347400	Strong transcription	HUVEC	blood vessel
14	chr6:86316000-86348600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:86316200-86339200	Strong transcription	Primary B cells from cord blood	blood
16	chr6:86316200-86347800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr6:86316200-86348600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr6:86316200-86348600	Strong transcription	Placenta	Placenta
19	chr6:86316200-86348800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:86316400-86348200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:86316400-86348400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr6:86316400-86349200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:86316400-86350600	Strong transcription	Fetal Thymus	thymus
24	chr6:86317000-86337400	Strong transcription	Primary T cells from cord blood	blood
25	chr6:86317000-86340400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:86317000-86349000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:86317400-86338800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr6:86317400-86349000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:86317600-86349800	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr6:86317800-86337600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:86317800-86348200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr6:86318600-86348800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr6:86318800-86347200	Strong transcription	Fetal Brain Female	brain
34	chr6:86319000-86350000	Strong transcription	Fetal Muscle Trunk	muscle
35	chr6:86319400-86348600	Strong transcription	K562	blood
36	chr6:86319600-86342400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr6:86319600-86348200	Strong transcription	NHEK	skin
38	chr6:86319600-86348800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:86319600-86350000	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr6:86320000-86344200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:86320000-86348600	Strong transcription	Liver	Liver
42	chr6:86320200-86335400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:86320200-86342400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:86320200-86350400	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr6:86320400-86337800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:86321000-86339200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:86321000-86348600	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:86321000-86349600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr6:86321200-86334600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr6:86321200-86334600	Strong transcription	Primary T killer memory cells from peripheral blood	blood

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