Variant report

Variant	rs3212229
Chromosome Location	chr6:24658394-24658395
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24656525..24658806-chr6:24716394..24719369,2	K562	blood:
2	chr6:24645670..24648708-chr6:24654981..24659486,5	MCF-7	breast:
3	chr6:24652247..24658784-chr6:24665384..24668018,7	MCF-7	breast:
4	chr6:24645396..24648552-chr6:24658188..24661192,4	K562	blood:
5	chr6:24657843..24659411-chr6:26030183..26032461,2	K562	blood:
6	chr6:24645396..24648521-chr6:24658092..24661192,3	K562	blood:
7	chr6:24657655..24659922-chr6:24720349..24722391,2	K562	blood:

Variant related genes	Relation type
ENSG00000137261	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000112308	Chromatin interaction
ENSG00000111802	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12662779	0.83[AMR][1000 genomes]
rs16889592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16901739	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17249687	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1883591	0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2056998	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2073013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2294688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2294689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2294690	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2294691	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2328847	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2876679	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3181230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3181233	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3181235	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3181236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3181237	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3212228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3212234	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3212235	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3756815	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4298343	1.00[CEU][hapmap]
rs60707509	0.83[AMR][1000 genomes]
rs7765052	0.87[ASN][1000 genomes]
rs9356944	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs9358786	0.88[ASN][1000 genomes]
rs9358787	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9366579	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9379682	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9379686	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs9393575	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9461050	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9467251	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9467253	0.86[ASN][1000 genomes]
rs9467257	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv601164	chr6:24625091-24661599	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv601165	chr6:24632642-24666007	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv883481	chr6:24652247-24659071	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24646400-24658800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:24646800-24662400	Weak transcription	Right Ventricle	heart
3	chr6:24646800-24662600	Weak transcription	Spleen	Spleen
4	chr6:24646800-24666000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:24647000-24659000	Weak transcription	Stomach Mucosa	stomach
6	chr6:24647000-24662200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:24647000-24662400	Weak transcription	Lung	lung
8	chr6:24647000-24662600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:24647000-24666400	Weak transcription	Esophagus	oesophagus
10	chr6:24647200-24663400	Weak transcription	Fetal Kidney	kidney
11	chr6:24649400-24659200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:24649400-24659600	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:24649400-24664800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:24649400-24665200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:24650000-24658400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:24650000-24658400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr6:24650000-24658600	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr6:24650000-24659000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr6:24650000-24663600	Strong transcription	Dnd41	blood
20	chr6:24650000-24665000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:24650200-24658800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:24650200-24659000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:24650200-24659000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr6:24650200-24659000	Strong transcription	Duodenum Mucosa	Duodenum
25	chr6:24650400-24658600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:24650600-24658800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr6:24651000-24659800	Strong transcription	Primary B cells from peripheral blood	blood
28	chr6:24651200-24659200	Weak transcription	Small Intestine	intestine
29	chr6:24652400-24662800	Weak transcription	Psoas Muscle	Psoas
30	chr6:24653200-24659000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:24653400-24658800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr6:24653400-24662600	Weak transcription	NHLF	lung
33	chr6:24653600-24659200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:24653600-24660000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:24653800-24658800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr6:24653800-24659000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:24653800-24659200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr6:24653800-24662200	Weak transcription	Fetal Stomach	stomach
39	chr6:24653800-24662200	Weak transcription	Ovary	ovary
40	chr6:24653800-24662400	Weak transcription	Colonic Mucosa	Colon
41	chr6:24653800-24662600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:24653800-24663800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:24653800-24666200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:24654000-24658400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr6:24654000-24658400	Weak transcription	Thymus	Thymus
46	chr6:24654000-24662600	Weak transcription	HSMMtube	muscle
47	chr6:24654000-24663200	Weak transcription	Fetal Brain Male	brain
48	chr6:24654000-24665200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr6:24654200-24659400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:24654200-24661600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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