Variant report

Variant	rs59049638
Chromosome Location	chr2:98613336-98613337
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	POLR2A	chr2:98611441-98613359	GM19193	blood:	n/a	n/a
2	POLR2A	chr2:98611431-98613532	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr2:98609735-98613766	GM12891	blood:	n/a	n/a
4	YY1	chr2:98611591-98613343	H1-hESC	embryonic stem cell:	n/a	chr2:98612180-98612194 chr2:98612720-98612731 chr2:98612215-98612224 chr2:98612645-98612667 chr2:98612183-98612192 chr2:98612649-98612669 chr2:98612186-98612195 chr2:98612378-98612400 chr2:98612180-98612189 chr2:98611781-98611795 chr2:98612657-98612667 chr2:98612215-98612229 chr2:98612181-98612192 chr2:98612746-98612757 chr2:98612377-98612389 chr2:98611842-98611856 chr2:98612702-98612716
5	MAX	chr2:98611450-98613354	A549	lung:	n/a	chr2:98612354-98612364 chr2:98612740-98612750 chr2:98612693-98612703
6	MXI1	chr2:98610792-98613428	SK-N-SH	brain:	n/a	n/a
7	REST	chr2:98611502-98613351	H1-neurons	neurons:	n/a	chr2:98612629-98612642 chr2:98612209-98612229
8	POLR2A	chr2:98610947-98613478	GM18505	blood:	n/a	n/a
9	YY1	chr2:98611457-98613425	SK-N-SH	brain:	n/a	chr2:98612180-98612194 chr2:98612720-98612731 chr2:98612215-98612224 chr2:98612645-98612667 chr2:98612183-98612192 chr2:98612649-98612669 chr2:98612186-98612195 chr2:98612378-98612400 chr2:98612180-98612189 chr2:98611781-98611795 chr2:98612657-98612667 chr2:98612215-98612229 chr2:98612181-98612192 chr2:98612746-98612757 chr2:98612377-98612389 chr2:98611842-98611856 chr2:98612702-98612716
10	ELF1	chr2:98611623-98613481	GM12878	blood:	n/a	chr2:98611782-98611794 chr2:98611861-98611873 chr2:98612676-98612685 chr2:98611919-98611928 chr2:98612180-98612189 chr2:98612204-98612216 chr2:98612219-98612231 chr2:98611843-98611855 chr2:98612183-98612192

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98612119..98614854-chr2:98702248..98705786,3	K562	blood:
2	chr2:98610350..98614892-chr2:98700211..98704879,10	MCF-7	breast:

Variant related genes	Relation type
TMEM131	TF binding region
ENSG00000168658	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs28641817	1.00[ASN][1000 genomes]
rs55853292	0.83[EUR][1000 genomes]
rs58690282	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59444417	0.83[EUR][1000 genomes]
rs59635122	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59752876	0.86[EUR][1000 genomes]
rs62156488	0.83[EUR][1000 genomes]
rs62156507	0.80[EUR][1000 genomes]
rs62156508	0.83[EUR][1000 genomes]
rs62156509	0.83[EUR][1000 genomes]
rs62156519	0.84[EUR][1000 genomes]
rs62156522	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62156523	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62156524	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62156525	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62156526	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62156527	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62156530	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62158265	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158266	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62158268	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62158269	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158270	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62158272	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6740424	0.85[ASN][1000 genomes]
rs73960433	0.84[EUR][1000 genomes]
rs73960435	0.86[EUR][1000 genomes]
rs7600204	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98609200-98613400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:98609800-98613400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:98610400-98613400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:98610400-98613400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:98610400-98613400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:98610800-98613600	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr2:98610800-98613600	Active TSS	Brain Hippocampus Middle	brain
8	chr2:98611000-98613400	Active TSS	Brain Germinal Matrix	brain
9	chr2:98611000-98613400	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr2:98611200-98613400	Active TSS	Fetal Brain Female	brain
11	chr2:98611200-98613600	Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr2:98611400-98613600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:98612800-98613400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr2:98612800-98613400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr2:98612800-98613400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr2:98612800-98613400	Enhancers	Small Intestine	intestine
17	chr2:98612800-98613400	Flanking Active TSS	Dnd41	blood
18	chr2:98613000-98613400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:98613000-98613400	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr2:98613000-98613600	Enhancers	Spleen	Spleen
21	chr2:98613200-98613400	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr2:98613200-98613400	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr2:98613200-98613400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:98613200-98613400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:98613200-98613400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:98613200-98613400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:98613200-98613400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:98613200-98613400	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr2:98613200-98613400	Enhancers	Colonic Mucosa	Colon
30	chr2:98613200-98613400	Enhancers	Fetal Intestine Small	intestine
31	chr2:98613200-98613400	Flanking Bivalent TSS/Enh	Thymus	Thymus
32	chr2:98613200-98613400	Enhancers	K562	blood
33	chr2:98613200-98613600	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr2:98613200-98613600	Enhancers	Primary B cells from cord blood	blood
35	chr2:98613200-98613600	Enhancers	Primary B cells from peripheral blood	blood
36	chr2:98613200-98613600	Enhancers	Primary T cells fromperipheralblood	blood
37	chr2:98613200-98613600	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr2:98613200-98613600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:98613200-98613600	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr2:98613200-98613600	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr2:98613200-98613600	Enhancers	Esophagus	oesophagus
42	chr2:98613200-98613600	Enhancers	Fetal Intestine Large	intestine
43	chr2:98613200-98613600	Enhancers	Fetal Muscle Trunk	muscle
44	chr2:98613200-98613600	Enhancers	Fetal Thymus	thymus
45	chr2:98613200-98613600	Enhancers	Pancreas	Pancrea
46	chr2:98613200-98613600	Enhancers	Psoas Muscle	Psoas
47	chr2:98613200-98613600	Enhancers	Right Ventricle	heart
48	chr2:98613200-98613600	Flanking Active TSS	GM12878-XiMat	blood
49	chr2:98613200-98613800	Enhancers	H1 Cell Line	embryonic stem cell
50	chr2:98613200-98613800	Enhancers	Stomach Mucosa	stomach

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