Variant report

Variant	rs6939049
Chromosome Location	chr6:4009723-4009724
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:3778613..3780646-chr6:4009358..4012011,2	K562	blood:
2	chr6:4007350..4010336-chr6:4010836..4013423,2	K562	blood:
3	chr6:4006763..4009757-chr6:4011766..4014574,3	K562	blood:
4	chr6:4008961..4014281-chr6:4016436..4019625,9	MCF-7	breast:
5	chr6:4005813..4011105-chr6:4019911..4024934,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf146-1	chr6:4006806-4020323	NONHSAT107264

Variant related genes	Relation type
ENSG00000230648	Chromatin interaction
ENSG00000272248	Chromatin interaction
ENSG00000112739	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1543355	1.00[JPT][hapmap]
rs1886334	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2181894	1.00[JPT][hapmap]
rs2745451	1.00[JPT][hapmap]
rs3747762	1.00[JPT][hapmap]
rs3761787	1.00[JPT][hapmap]
rs4959915	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6421941	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6597023	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6597024	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6906467	1.00[JPT][hapmap]
rs6918566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924389	1.00[JPT][hapmap];0.87[YRI][hapmap]
rs697745	1.00[JPT][hapmap]
rs707980	1.00[JPT][hapmap]
rs707981	1.00[JPT][hapmap]
rs707982	1.00[JPT][hapmap]
rs707983	1.00[JPT][hapmap]
rs707985	1.00[JPT][hapmap]
rs7763721	0.92[ASN][1000 genomes]
rs853396	1.00[JPT][hapmap]
rs853397	1.00[JPT][hapmap]
rs853398	1.00[JPT][hapmap]
rs853400	1.00[JPT][hapmap]
rs853401	0.87[YRI][hapmap]
rs853403	1.00[JPT][hapmap]
rs853405	1.00[JPT][hapmap]
rs853406	1.00[JPT][hapmap]
rs853407	0.92[JPT][hapmap]
rs853408	1.00[JPT][hapmap]
rs853411	1.00[JPT][hapmap]
rs9328213	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9328215	1.00[JPT][hapmap]
rs9328216	1.00[JPT][hapmap]
rs9378394	0.90[ASN][1000 genomes]
rs9405690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9503893	1.00[JPT][hapmap]

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	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	56 gene(s)	inside rSNPs	diseases
4	esv1800199	chr6:3986611-4014872	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:3985400-4011000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:3991200-4010400	Weak transcription	K562	blood
3	chr6:3991200-4011000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:3991200-4012200	Weak transcription	Left Ventricle	heart
5	chr6:3991400-4011000	Weak transcription	Lung	lung
6	chr6:3991400-4016800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:3991600-4017200	Weak transcription	Fetal Brain Female	brain
8	chr6:3991600-4017400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:3991600-4017600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:3991800-4016600	Weak transcription	Aorta	Aorta
11	chr6:3991800-4017400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:3991800-4017400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr6:3991800-4017600	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:3993200-4011000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:3997400-4016200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:3997400-4017400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:3997600-4017600	Weak transcription	Psoas Muscle	Psoas
18	chr6:3997800-4010800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:3997800-4011000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:3998000-4017400	Weak transcription	NHLF	lung
21	chr6:3998200-4017400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:3998400-4016200	Weak transcription	Brain Germinal Matrix	brain
23	chr6:3998400-4017600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:3998400-4017600	Weak transcription	Small Intestine	intestine
25	chr6:3998600-4012800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:3998800-4017400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr6:4000200-4017400	Weak transcription	HUVEC	blood vessel
28	chr6:4000800-4013400	Weak transcription	Placenta	Placenta
29	chr6:4001400-4011000	Weak transcription	Thymus	Thymus
30	chr6:4001400-4016000	Weak transcription	Hela-S3	cervix
31	chr6:4002400-4011000	Weak transcription	Dnd41	blood
32	chr6:4002600-4010800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:4002800-4010400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:4003400-4010200	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr6:4004000-4011000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:4004000-4011000	Weak transcription	Spleen	Spleen
37	chr6:4004200-4013400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:4004400-4011000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr6:4004400-4016200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr6:4004600-4010800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:4004800-4010400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:4004800-4010800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr6:4004800-4011000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr6:4004800-4011000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:4004800-4012200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:4004800-4012600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:4005000-4010800	Weak transcription	Primary B cells from cord blood	blood
48	chr6:4005000-4011000	Weak transcription	Fetal Thymus	thymus
49	chr6:4005000-4016200	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:4005600-4011000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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