Variant report

Variant	rs17006680
Chromosome Location	chr3:20198854-20198855
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20195965..20199003-chr3:20200424..20204373,5	K562	blood:
2	chr3:20197490..20199260-chr3:20227955..20230018,2	K562	blood:
3	chr3:20197560..20199783-chr3:20225608..20228182,2	MCF-7	breast:
4	chr3:20197127..20199080-chr3:20208900..20210840,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129810	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10510498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1581002	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17006645	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17006684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17006703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17006705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17006760	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17006762	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17497321	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2292226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292227	1.00[CEU][hapmap]
rs2292229	1.00[ASN][1000 genomes]
rs3762631	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3804573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60747537	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs61280687	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6783444	1.00[CEU][hapmap]
rs6792672	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9310614	0.90[ASN][1000 genomes]
rs9878045	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	esv1829018	chr3:20116077-20596244	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	esv1827700	chr3:20119716-20489086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	esv1830036	chr3:20121828-20278275	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
13	esv1830599	chr3:20121828-20375643	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	esv1828816	chr3:20136508-20389045	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
15	esv3394910	chr3:20150394-20203576	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
16	esv3334928	chr3:20150414-20203546	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
17	esv1832674	chr3:20152772-20605302	Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
18	esv1831853	chr3:20157077-20615273	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
19	esv1833208	chr3:20157077-20638228	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
20	esv2422249	chr3:20163608-20626956	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
21	esv1826144	chr3:20164282-20638228	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
22	nsv1013532	chr3:20172889-20305612	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
23	nsv536513	chr3:20172889-20305612	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
24	esv1831289	chr3:20191506-20617984	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
25	esv1829973	chr3:20192578-20375260	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
26	esv1829847	chr3:20196923-20638228	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
27	nsv876597	chr3:20197364-20242143	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20141200-20222400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:20159200-20201400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:20164400-20204400	Weak transcription	Small Intestine	intestine
4	chr3:20164800-20211400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:20167800-20226000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:20168800-20200800	Weak transcription	GM12878-XiMat	blood
7	chr3:20169800-20201600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:20169800-20202000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:20181800-20200200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:20182600-20201400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:20183600-20201000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:20183800-20199600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:20183800-20199600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:20184400-20199000	Weak transcription	Esophagus	oesophagus
15	chr3:20184600-20220200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:20187400-20201000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr3:20187600-20201200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:20188400-20204800	Weak transcription	Fetal Brain Female	brain
19	chr3:20188400-20212400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:20189600-20200800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:20189800-20201600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr3:20190000-20199600	Weak transcription	A549	lung
23	chr3:20190200-20201400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:20190200-20201800	Weak transcription	Fetal Intestine Large	intestine
25	chr3:20190400-20202400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:20190600-20220200	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:20191000-20199400	Weak transcription	Brain Substantia Nigra	brain
28	chr3:20191200-20200800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:20191600-20199000	Weak transcription	Placenta	Placenta
30	chr3:20191600-20201200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr3:20191600-20201400	Weak transcription	Left Ventricle	heart
32	chr3:20191800-20200800	Weak transcription	HSMM	muscle
33	chr3:20191800-20201800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:20191800-20201800	Weak transcription	Adipose Nuclei	Adipose
35	chr3:20191800-20202400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr3:20191800-20202600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:20192400-20199800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:20192400-20200800	Weak transcription	Fetal Heart	heart
39	chr3:20192400-20201800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:20192800-20220600	Weak transcription	Fetal Lung	lung
41	chr3:20193000-20201800	Weak transcription	Colon Smooth Muscle	Colon
42	chr3:20193200-20204000	Strong transcription	Fetal Thymus	thymus
43	chr3:20193400-20200600	Weak transcription	Hela-S3	cervix
44	chr3:20193800-20226600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr3:20194000-20220400	Weak transcription	NH-A	brain
46	chr3:20194200-20201600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:20194200-20205400	Strong transcription	Dnd41	blood
48	chr3:20194800-20215200	Weak transcription	HepG2	liver
49	chr3:20195000-20200200	Weak transcription	HMEC	breast
50	chr3:20195000-20212400	Weak transcription	H9 Cell Line	embryonic stem cell

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