Variant report

Variant	rs16846293
Chromosome Location	chr1:224486889-224486890
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	ZNF217	chr1:224486714-224487071	MCF-7	breast:	n/a	n/a
2	GATA3	chr1:224486583-224487115	MCF-7	breast:	n/a	chr1:224486659-224486666 chr1:224486657-224486667 chr1:224486654-224486670 chr1:224486867-224486880 chr1:224486657-224486666
3	GATA2	chr1:224486693-224486893	SH-SY5Y	brain:	n/a	chr1:224486867-224486880
4	GATA3	chr1:224486481-224487046	SH-SY5Y	brain:	n/a	chr1:224486659-224486666 chr1:224486657-224486667 chr1:224486654-224486670 chr1:224486867-224486880 chr1:224486657-224486666
5	GATA3	chr1:224486634-224487170	MCF-7	breast:	n/a	chr1:224486659-224486666 chr1:224486657-224486667 chr1:224486654-224486670 chr1:224486867-224486880 chr1:224486657-224486666
6	GATA3	chr1:224486563-224487193	MCF-7	breast:	n/a	chr1:224486659-224486666 chr1:224486657-224486667 chr1:224486654-224486670 chr1:224486867-224486880 chr1:224486657-224486666
7	TCF7L2	chr1:224486724-224487032	MCF-7	breast:	n/a	n/a
8	SIN3AK20	chr1:224486564-224487487	MCF-7	breast:	n/a	n/a
9	GATA3	chr1:224486674-224487044	MCF-7	breast:	n/a	chr1:224486867-224486880
10	NR2F2	chr1:224486695-224487197	MCF-7	breast:	n/a	n/a
11	GATA3	chr1:224486605-224486987	T-47D	breast:	n/a	chr1:224486659-224486666 chr1:224486657-224486667 chr1:224486654-224486670 chr1:224486867-224486880 chr1:224486657-224486666
12	EP300	chr1:224486668-224487187	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:224300765..224303424-chr1:224486514..224488208,2	MCF-7	breast:
2	chr1:224485820..224488215-chr1:224499700..224501830,2	MCF-7	breast:
3	chr1:224486717..224491165-chr1:224492044..224494340,5	MCF-7	breast:
4	chr1:224485304..224486995-chr1:224491805..224493803,2	MCF-7	breast:

Variant related genes	Relation type
NVL	TF binding region
ENSG00000143748	Chromatin interaction
ENSG00000206887	Chromatin interaction
ENSG00000143756	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10495221	1.00[EUR][1000 genomes]
rs10799556	0.92[ASW][hapmap];1.00[MEX][hapmap]
rs11801211	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11802182	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11807149	1.00[EUR][1000 genomes]
rs11809688	1.00[EUR][1000 genomes]
rs11809710	0.85[ASW][hapmap];1.00[EUR][1000 genomes]
rs11810160	1.00[EUR][1000 genomes]
rs11811935	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11812007	1.00[EUR][1000 genomes]
rs12239235	1.00[EUR][1000 genomes]
rs12239466	1.00[EUR][1000 genomes]
rs1401319	1.00[EUR][1000 genomes]
rs1499284	1.00[EUR][1000 genomes]
rs16845729	0.82[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16845878	0.81[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16846190	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846212	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846339	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs16846494	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847675	1.00[EUR][1000 genomes]
rs16847784	1.00[EUR][1000 genomes]
rs16847858	1.00[EUR][1000 genomes]
rs16847867	0.85[ASW][hapmap]
rs16847870	1.00[EUR][1000 genomes]
rs16847871	1.00[EUR][1000 genomes]
rs1857042	1.00[EUR][1000 genomes]
rs2068945	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2794805	1.00[EUR][1000 genomes]
rs4653586	1.00[EUR][1000 genomes]
rs55712053	1.00[EUR][1000 genomes]
rs57027684	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57469223	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57719044	1.00[EUR][1000 genomes]
rs57967341	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58304668	1.00[EUR][1000 genomes]
rs58649883	1.00[EUR][1000 genomes]
rs58788859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58814229	1.00[EUR][1000 genomes]
rs58954846	1.00[EUR][1000 genomes]
rs59236258	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59561838	1.00[EUR][1000 genomes]
rs59577766	1.00[EUR][1000 genomes]
rs59710928	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60349703	1.00[EUR][1000 genomes]
rs60627429	1.00[EUR][1000 genomes]
rs60715845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60831135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61000820	1.00[EUR][1000 genomes]
rs61056357	1.00[EUR][1000 genomes]
rs61155217	1.00[EUR][1000 genomes]
rs61162360	1.00[EUR][1000 genomes]
rs61278437	1.00[EUR][1000 genomes]
rs6426167	1.00[EUR][1000 genomes]
rs6659109	1.00[EUR][1000 genomes]
rs6664674	1.00[EUR][1000 genomes]
rs6674133	1.00[EUR][1000 genomes]
rs6681611	1.00[EUR][1000 genomes]
rs6687424	1.00[EUR][1000 genomes]
rs6702649	1.00[EUR][1000 genomes]
rs73121865	1.00[EUR][1000 genomes]
rs73122500	1.00[EUR][1000 genomes]
rs73123788	1.00[EUR][1000 genomes]
rs73123791	1.00[EUR][1000 genomes]
rs73124468	1.00[EUR][1000 genomes]
rs73124491	1.00[EUR][1000 genomes]
rs73124493	1.00[EUR][1000 genomes]
rs73125526	1.00[EUR][1000 genomes]
rs73125529	1.00[EUR][1000 genomes]
rs73126411	1.00[EUR][1000 genomes]
rs73128442	1.00[EUR][1000 genomes]
rs74146372	1.00[EUR][1000 genomes]
rs74146374	1.00[EUR][1000 genomes]
rs74146377	1.00[EUR][1000 genomes]
rs7512165	1.00[EUR][1000 genomes]
rs7514645	1.00[MEX][hapmap]
rs7525250	1.00[MEX][hapmap]
rs7531588	1.00[ASW][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic 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	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224431200-224490400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:224433400-224516200	Weak transcription	Fetal Heart	heart
3	chr1:224439800-224501600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:224461200-224505600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr1:224465000-224487600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:224465000-224488000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:224465000-224504400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:224465000-224504400	Strong transcription	Liver	Liver
9	chr1:224465000-224505200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:224465000-224505600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:224465200-224487000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:224465400-224505600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:224466200-224487800	Strong transcription	NH-A	brain
14	chr1:224466400-224505400	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr1:224466400-224505400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:224466400-224505600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr1:224466600-224505600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:224466800-224499200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:224468000-224505200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:224468200-224496000	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:224468600-224500000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr1:224469800-224493200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:224473000-224496200	Strong transcription	Dnd41	blood
24	chr1:224473200-224497400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:224473600-224505400	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:224473600-224505400	Strong transcription	Fetal Thymus	thymus
27	chr1:224474000-224488000	Strong transcription	Primary B cells from cord blood	blood
28	chr1:224474400-224497200	Weak transcription	Stomach Mucosa	stomach
29	chr1:224474600-224496000	Strong transcription	Adipose Nuclei	Adipose
30	chr1:224474600-224498000	Strong transcription	Primary T cells from cord blood	blood
31	chr1:224475600-224505800	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:224476000-224496200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:224476000-224505600	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:224476000-224506200	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:224476400-224505600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:224476600-224500000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:224476600-224505600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:224476600-224506200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:224477400-224505800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:224478000-224499600	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr1:224478400-224496000	Strong transcription	K562	blood
42	chr1:224478400-224501000	Strong transcription	Duodenum Mucosa	Duodenum
43	chr1:224478400-224504800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr1:224478400-224505400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:224478600-224488000	Strong transcription	Osteobl	bone
46	chr1:224478600-224496000	Strong transcription	Primary hematopoietic stem cells	blood
47	chr1:224478600-224498200	Strong transcription	Fetal Brain Female	brain
48	chr1:224478600-224500600	Strong transcription	Fetal Muscle Leg	muscle
49	chr1:224478800-224491800	Strong transcription	Rectal Smooth Muscle	rectum
50	chr1:224478800-224505200	Strong transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links