Variant report

Variant	rs2235716
Chromosome Location	chr6:1607116-1607117
allele	C/T
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	USF2	chr6:1606904-1607294	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTBP2	chr6:1605896-1607554	H1-hESC	embryonic stem cell:	n/a	n/a
3	JUND	chr6:1607111-1608115	H1-hESC	embryonic stem cell:	n/a	chr6:1607276-1607285
4	RAD21	chr6:1606999-1607425	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:1607075-1607162	Hela-S3	cervix:	n/a	n/a
6	SP1	chr6:1606816-1607552	H1-hESC	embryonic stem cell:	n/a	chr6:1607346-1607360 chr6:1607349-1607361 chr6:1607346-1607355 chr6:1607538-1607545
7	TEAD4	chr6:1606941-1607444	H1-hESC	embryonic stem cell:	n/a	chr6:1607157-1607166
8	ZNF263	chr6:1606891-1610222	HEK293-T-REx	kidney:	n/a	chr6:1607928-1607937 chr6:1607926-1607947
9	TCF7L2	chr6:1607037-1608244	HEK293	kidney:	n/a	n/a
10	CHD2	chr6:1606833-1608130	H1-hESC	embryonic stem cell:	n/a	n/a
11	EP300	chr6:1607017-1607386	H1-hESC	embryonic stem cell:	n/a	chr6:1607081-1607095 chr6:1607086-1607100 chr6:1607079-1607093 chr6:1607340-1607356
12	TEAD4	chr6:1606965-1607460	H1-hESC	embryonic stem cell:	n/a	chr6:1607157-1607166
13	TCF12	chr6:1606952-1607405	H1-hESC	embryonic stem cell:	n/a	n/a
14	SP1	chr6:1607009-1607598	H1-hESC	embryonic stem cell:	n/a	chr6:1607346-1607360 chr6:1607349-1607361 chr6:1607346-1607355 chr6:1607538-1607545
15	POLR2A	chr6:1606446-1612572	HEK293	kidney:	n/a	n/a
16	SIN3A	chr6:1607105-1609176	H1-hESC	embryonic stem cell:	n/a	chr6:1608712-1608720 chr6:1608414-1608427 chr6:1608395-1608406
17	SUZ12	chr6:1604488-1607142	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr6:1607071-1609341	H1-neurons	neurons:	n/a	n/a
19	USF1	chr6:1607054-1607369	H1-hESC	embryonic stem cell:	n/a	n/a
20	KAP1	chr6:1606958-1608730	HEK293	kidney:	n/a	n/a
21	CREB1	chr6:1606950-1607568	H1-hESC	embryonic stem cell:	n/a	chr6:1607274-1607287
22	ZNF143	chr6:1607108-1607374	H1-hESC	embryonic stem cell:	n/a	chr6:1607339-1607357
23	KAP1	chr6:1607001-1607319	U2OS	brain:	n/a	n/a
24	TBP	chr6:1607042-1607389	H1-hESC	embryonic stem cell:	n/a	n/a
25	HDAC2	chr6:1607030-1607402	H1-hESC	embryonic stem cell:	n/a	chr6:1607081-1607095 chr6:1607083-1607097 chr6:1607080-1607094 chr6:1607082-1607096 chr6:1607078-1607092
26	USF1	chr6:1606944-1607290	H1-hESC	embryonic stem cell:	n/a	n/a
27	CREB1	chr6:1607065-1607491	H1-hESC	embryonic stem cell:	n/a	chr6:1607274-1607287

No.	Distal block	Cell Line	Cell type
1	chr6:1606529..1608370-chr6:1661699..1664667,2	MCF-7	breast:
2	chr6:1605093..1609098-chr6:1671097..1673871,3	MCF-7	breast:
3	chr6:1606456..1608668-chr6:2173309..2175661,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXC1-1	chr6:1606251-1607305	XLOC_005125
2	lnc-GMDS-6	chr6:1603265-1608466	NONHSAT106529
3	lnc-GMDS-6	chr6:1605088-1607351	NONHSAT106531
4	lnc-FOXC1-1	chr6:1606251-1607583	NONHSAT106530

Variant related genes	Relation type
FOXC1	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs34903038	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024111	chr6:1231850-1730146	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1021924	chr6:1254891-1736995	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv538082	chr6:1254891-1736995	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv917248	chr6:1365437-1627813	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1034039	chr6:1427061-1691837	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv538088	chr6:1427061-1691837	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
8	nsv1027393	chr6:1446300-1692019	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv538089	chr6:1446300-1692019	Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv1016859	chr6:1460020-1645819	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv883376	chr6:1535043-1635082	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv1016594	chr6:1590030-1702529	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
14	nsv823394	chr6:1590091-1629146	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
15	nsv883378	chr6:1593851-1623990	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
16	nsv883379	chr6:1593851-1628902	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
17	nsv823395	chr6:1595031-1629521	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
18	nsv883380	chr6:1595216-1621404	Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
19	nsv883381	chr6:1595216-1628902	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
20	nsv823396	chr6:1597359-1629106	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
21	nsv883382	chr6:1598942-1620037	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
22	nsv823397	chr6:1603867-1622264	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
23	nsv530888	chr6:1605768-1739933	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1604200-1610800	Active TSS	Aorta	Aorta
2	chr6:1604400-1610800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:1604800-1609600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
4	chr6:1605000-1607400	Bivalent Enhancer	GM12878-XiMat	blood
5	chr6:1605000-1607600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
6	chr6:1605000-1609400	Bivalent Enhancer	Fetal Thymus	thymus
7	chr6:1605000-1610800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr6:1605200-1608800	Weak transcription	Hela-S3	cervix
9	chr6:1605200-1609600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
10	chr6:1605400-1607800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:1605400-1608000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
12	chr6:1605400-1609000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:1605400-1609000	Weak transcription	HMEC	breast
14	chr6:1605400-1609400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
15	chr6:1605400-1609400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:1605400-1609400	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr6:1605600-1607200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
18	chr6:1605600-1607800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:1605600-1607800	Weak transcription	Gastric	stomach
20	chr6:1605600-1609000	Enhancers	Pancreas	Pancrea
21	chr6:1605600-1609000	Weak transcription	Right Atrium	heart
22	chr6:1605600-1609400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
23	chr6:1605600-1620800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:1605800-1607200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
25	chr6:1605800-1607600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
26	chr6:1605800-1607600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:1605800-1608000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
28	chr6:1605800-1608000	Bivalent Enhancer	NHDF-Ad	bronchial
29	chr6:1605800-1608600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
30	chr6:1606000-1607200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:1606000-1607200	Bivalent Enhancer	HepG2	liver
32	chr6:1606000-1607400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:1606000-1607600	Bivalent Enhancer	Primary T cells from cord blood	blood
34	chr6:1606000-1607600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
35	chr6:1606200-1609800	Bivalent/Poised TSS	Fetal Kidney	kidney
36	chr6:1606400-1607200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:1606400-1607800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:1606400-1607800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
39	chr6:1606600-1607200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr6:1606600-1607200	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:1606600-1607200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr6:1606600-1607400	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
43	chr6:1606600-1608600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
44	chr6:1606800-1607200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:1606800-1607200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:1606800-1607400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:1606800-1607400	Bivalent Enhancer	Lung	lung
48	chr6:1606800-1607600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
49	chr6:1606800-1607800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
50	chr6:1606800-1608000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin

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