Variant report

Variant	rs17069446
Chromosome Location	chr6:140203051-140203052
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:140202874-140203174	MCF-7	breast:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
2	CTCF	chr6:140202920-140203070	HFF	foreskin:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
3	CTCF	chr6:140202882-140203108	K562	blood:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
4	CTCF	chr6:140202940-140203090	BJ	skin:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
5	CTCF	chr6:140202842-140203106	Medullo	brain:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
6	CTCF	chr6:140202872-140203108	Hela-S3	cervix:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
7	CTCF	chr6:140202920-140203070	GM12873	blood:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
8	CTCF	chr6:140202889-140203087	GM10266	blood:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
9	CTCF	chr6:140202867-140203154	MCF-7	breast:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
10	CTCF	chr6:140202960-140203110	WERI-Rb-1	eye:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
11	RAD21	chr6:140202700-140203436	HCT-116	colon:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006
12	CTCF	chr6:140202890-140203060	ProgFib	skin:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
13	CTCF	chr6:140202874-140203115	Gliobla	brain:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
14	RAD21	chr6:140202765-140203248	GM12878	blood:	n/a	chr6:140203206-140203220 chr6:140202987-140203006
15	CTCF	chr6:140202940-140203090	GM12867	blood:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
16	BRCA1	chr6:140202877-140203121	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr6:140202890-140203094	GM13977	blood:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
18	SMC3	chr6:140202835-140203241	K562	blood:	n/a	n/a
19	CTCF	chr6:140202725-140203171	K562	blood:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
20	CTCF	chr6:140202920-140203070	AG10803	skin:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
21	CTCF	chr6:140202920-140203070	GM12864	blood:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
22	CTCF	chr6:140202920-140203070	HEEpiC	esophagus:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
23	CTCF	chr6:140202920-140203070	AG04450	lung:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
24	RAD21	chr6:140202771-140203285	A549	lung:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006
25	RAD21	chr6:140202830-140203424	HCT-116	colon:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006
26	TEAD4	chr6:140202856-140203196	H1-hESC	embryonic stem cell:	n/a	n/a
27	RAD21	chr6:140202644-140203346	MCF-7	breast:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006
28	CTCF	chr6:140202841-140203117	HUVEC	blood vessel:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
29	ARID3A	chr6:140202803-140203064	K562	blood:	n/a	n/a
30	CHD2	chr6:140202802-140203204	H1-hESC	embryonic stem cell:	n/a	n/a
31	BACH1	chr6:140202977-140203164	K562	blood:	n/a	n/a
32	CTCF	chr6:140202830-140203339	A549	lung:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
33	CTCF	chr6:140202879-140203072	GM10248	blood:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
34	CTCF	chr6:140202940-140203090	HCFaa	heart:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
35	CTCF	chr6:140202920-140203070	GM06990	blood:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
36	CTCF	chr6:140202832-140203258	K562	blood:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
37	CTCF	chr6:140202920-140203070	Hela-S3	cervix:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
38	CTCF	chr6:140202769-140203154	SK-N-SH_RA	brain:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
39	CTCF	chr6:140202886-140203086	NHEK	skin:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
40	CTCF	chr6:140202940-140203090	K562	blood:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
41	CTCF	chr6:140202844-140203180	H1-hESC	embryonic stem cell:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
42	CTCF	chr6:140202909-140203087	Fibrobl	skin:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
43	CTCF	chr6:140202940-140203090	GM12872	blood:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
44	RAD21	chr6:140202712-140203439	H1-hESC	embryonic stem cell:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006
45	CTCF	chr6:140202872-140203124	GM12878	blood:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
46	CTCF	chr6:140202960-140203110	GM12874	blood:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
47	GATA3	chr6:140202692-140203771	SK-N-SH	brain:	n/a	chr6:140203511-140203520 chr6:140203410-140203421 chr6:140203709-140203719 chr6:140203510-140203520
48	CTCF	chr6:140202980-140203130	A549	lung:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
49	CTCF	chr6:140202940-140203090	GM12864	blood:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
50	SMC3	chr6:140202771-140203209	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:140202746..140205528-chr6:140208165..140210292,2	K562	blood:
2	chr6:139692335..139698075-chr6:140197375..140205470,17	MCF-7	breast:
3	chr6:140202740..140203385-chr6:140317580..140318152,2	MCF-7	breast:
4	chr6:140202203..140203486-chr6:140248180..140248949,4	MCF-7	breast:
5	chr6:140202949..140203456-chr6:141242488..141243293,2	MCF-7	breast:
6	chr6:140202515..140205528-chr6:140208165..140211710,3	K562	blood:
7	chr6:140202585..140203697-chr6:140762103..140763026,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225148	TF binding region
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1028472	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484811	0.95[YRI][hapmap]
rs11751210	1.00[JPT][hapmap]
rs11756192	1.00[JPT][hapmap]
rs11758188	1.00[JPT][hapmap]
rs17069431	0.85[YRI][hapmap]
rs17069449	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17069457	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17069468	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17069471	0.95[YRI][hapmap]
rs17069477	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17069489	0.95[YRI][hapmap]
rs17516817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17755520	1.00[JPT][hapmap]
rs17811871	1.00[JPT][hapmap]
rs17812617	1.00[JPT][hapmap]
rs17812647	1.00[JPT][hapmap]
rs1890428	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1963700	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4895575	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895576	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895577	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4895580	1.00[JPT][hapmap]
rs4896497	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896498	1.00[ASN][1000 genomes]
rs4896499	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896500	1.00[ASN][1000 genomes]
rs4896502	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs56690523	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60716022	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656363	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6570385	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6570386	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908754	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6913694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6921596	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921645	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73563232	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73563265	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73563279	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[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	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
5	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140190800-140203400	Weak transcription	Fetal Lung	lung
2	chr6:140194800-140204200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:140201000-140206400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:140201200-140203200	Weak transcription	Placenta	Placenta
5	chr6:140201400-140203400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:140201400-140204200	Weak transcription	Liver	Liver
7	chr6:140201800-140203200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:140201800-140203200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:140201800-140205000	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr6:140201800-140206400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:140202000-140203200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:140202000-140203800	Enhancers	Brain Germinal Matrix	brain
13	chr6:140202000-140209000	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr6:140202000-140209600	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr6:140202200-140204400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:140202200-140205000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr6:140202200-140206400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr6:140202400-140203200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:140202400-140203200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr6:140202400-140203200	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr6:140202400-140203400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:140202400-140203600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:140202400-140203800	Weak transcription	Fetal Kidney	kidney
24	chr6:140202400-140204000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:140202400-140205000	Enhancers	Brain Anterior Caudate	brain
26	chr6:140202400-140205200	Enhancers	Brain Substantia Nigra	brain
27	chr6:140202400-140205400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr6:140202400-140205600	Enhancers	Fetal Heart	heart
29	chr6:140202400-140205600	Enhancers	HSMM	muscle
30	chr6:140202400-140206000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:140202400-140206400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr6:140202400-140211800	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr6:140202600-140203200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:140202600-140205200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:140202600-140205800	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr6:140202600-140206400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr6:140202800-140203400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr6:140203000-140203200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:140203000-140203200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:140203000-140203200	Enhancers	Adipose Nuclei	Adipose
41	chr6:140203000-140203200	Flanking Active TSS	Brain Hippocampus Middle	brain
42	chr6:140203000-140203200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr6:140203000-140203200	Enhancers	NH-A	brain
44	chr6:140203000-140203200	Enhancers	NHLF	lung
45	chr6:140203000-140203400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:140203000-140203400	Enhancers	Stomach Smooth Muscle	stomach
47	chr6:140203000-140203400	Enhancers	Spleen	Spleen
48	chr6:140203000-140203400	Enhancers	A549	lung
49	chr6:140203000-140203800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr6:140203000-140203800	Enhancers	Fetal Muscle Trunk	muscle

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