Variant report

Variant	rs2256507
Chromosome Location	chr19:44038306-44038307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:44036740..44039638-chr19:44122133..44124023,3	MCF-7	breast:
2	chr19:43967717..43971076-chr19:44036987..44039699,3	MCF-7	breast:
3	chr19:44036787..44038928-chr19:44171420..44173895,2	K562	blood:
4	chr19:44036203..44038928-chr19:44171420..44174647,3	K562	blood:
5	chr19:44037962..44039566-chr19:44122300..44125209,2	MCF-7	breast:
6	chr19:44007568..44009583-chr19:44036201..44039639,3	MCF-7	breast:
7	chr19:44036629..44040127-chr19:44122528..44124622,4	K562	blood:
8	chr19:44036790..44040633-chr19:44098075..44102401,5	K562	blood:
9	chr19:44038066..44039609-chr19:44044499..44046745,2	K562	blood:
10	chr19:43937232..43939100-chr19:44037778..44039902,2	MCF-7	breast:
11	chr19:44036790..44039764-chr19:44099068..44102401,4	K562	blood:
12	chr19:44036736..44038487-chr19:44172015..44174560,2	MCF-7	breast:
13	chr19:44029247..44034379-chr19:44035166..44038879,9	MCF-7	breast:
14	chr19:44036786..44040035-chr19:44171480..44174677,5	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-L34079.1-4	chr19:44037947-44038418	NONHSAT066599

No data

Variant related genes	Relation type
ENSG00000105755	Chromatin interaction
ENSG00000176531	Chromatin interaction
ENSG00000176472	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000124466	Chromatin interaction
ENSG00000131116	Chromatin interaction
ENSG00000226763	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000011422	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1001581	0.92[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs12608635	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12611088	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12978269	0.82[JPT][hapmap]
rs1799778	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2261316	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs2305375	0.88[JPT][hapmap]
rs25486	0.81[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs25487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2599447	0.88[JPT][hapmap]
rs2599454	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2599455	0.82[ASN][1000 genomes]
rs2599456	0.81[ASN][1000 genomes]
rs2599463	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2599465	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2682559	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2682566	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2682578	0.88[JPT][hapmap]
rs3810378	0.88[CEU][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58617453	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6509092	0.88[JPT][hapmap]
rs6509096	0.83[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs8110232	0.88[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS 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 target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats 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 target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1056785	chr19:44010370-44081601	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv912107	chr19:44030998-44055726	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2256507	ZNF649	cis	parietal	SCAN
rs2256507	IL4I1	cis	cerebellum	SCAN
rs2256507	CD37	cis	parietal	SCAN
rs2256507	SLC17A7	cis	cerebellum	SCAN
rs2256507	ZNF575	cis	lung	GTEx
rs2256507	SIGLEC7	cis	parietal	SCAN
rs2256507	BCAT2	cis	parietal	SCAN
rs2256507	TEAD2	cis	parietal	SCAN
rs2256507	IZUMO1	cis	cerebellum	SCAN
rs2256507	BCAT2	cis	cerebellum	SCAN
rs2256507	TRPM4	cis	cerebellum	SCAN
rs2256507	SLC8A2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44036400-44038400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:44036400-44038400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr19:44036400-44038600	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr19:44036400-44038600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr19:44036400-44038800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr19:44036400-44038800	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr19:44036400-44039000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:44036400-44039000	Active TSS	Brain Angular Gyrus	brain
9	chr19:44036600-44038400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr19:44036600-44038400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr19:44036600-44038400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr19:44036600-44038400	Active TSS	Brain Anterior Caudate	brain
13	chr19:44036600-44038400	Active TSS	Psoas Muscle	Psoas
14	chr19:44036600-44038600	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr19:44036600-44038600	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr19:44036600-44038600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr19:44036600-44038600	Active TSS	Aorta	Aorta
18	chr19:44036600-44038600	Flanking Active TSS	Placenta	Placenta
19	chr19:44036600-44038600	Active TSS	Right Atrium	heart
20	chr19:44036600-44038800	Active TSS	H9 Cell Line	embryonic stem cell
21	chr19:44036600-44038800	Active TSS	Fetal Kidney	kidney
22	chr19:44036600-44038800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr19:44036600-44038800	Flanking Active TSS	HMEC	breast
24	chr19:44036600-44040200	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr19:44036800-44038600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr19:44036800-44038600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:44036800-44038600	Active TSS	Ovary	ovary
28	chr19:44037000-44038400	Active TSS	Fetal Intestine Small	intestine
29	chr19:44037000-44038400	Active TSS	Fetal Stomach	stomach
30	chr19:44037000-44038400	Active TSS	Rectal Smooth Muscle	rectum
31	chr19:44037000-44038400	Active TSS	Spleen	Spleen
32	chr19:44037000-44038600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:44037000-44038600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr19:44037000-44038600	Active TSS	Brain Substantia Nigra	brain
35	chr19:44037000-44038600	Active TSS	Colon Smooth Muscle	Colon
36	chr19:44037000-44038600	Active TSS	Fetal Intestine Large	intestine
37	chr19:44037000-44038800	Active TSS	H1 Cell Line	embryonic stem cell
38	chr19:44037000-44038800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:44037000-44038800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:44037000-44038800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:44037000-44038800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr19:44037000-44038800	Active TSS	Brain Cingulate Gyrus	brain
43	chr19:44037000-44038800	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr19:44037000-44038800	Active TSS	Duodenum Mucosa	Duodenum
45	chr19:44037000-44038800	Active TSS	HSMM	muscle
46	chr19:44037000-44038800	Active TSS	NHDF-Ad	bronchial
47	chr19:44037000-44039000	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr19:44037000-44039400	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr19:44037200-44038400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:44037200-44038400	Active TSS	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links