Variant report

Variant	rs41350144
Chromosome Location	chr1:61815799-61815800
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:61815740-61815890	GM12864	blood:	n/a	n/a
2	RAD21	chr1:61815599-61816079	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr1:61815770-61816011	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr1:61815732-61815999	K562	blood:	n/a	n/a
5	CTCF	chr1:61815760-61815910	GM12873	blood:	n/a	n/a
6	CTCF	chr1:61815780-61815930	GM12865	blood:	n/a	n/a
7	CTCF	chr1:61815760-61815910	HCPEpiC	choroid plexus:	n/a	n/a
8	CTCF	chr1:61815795-61815954	GM12878	blood:	n/a	n/a
9	RAD21	chr1:61815710-61815969	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr1:61815760-61815910	GM12872	blood:	n/a	n/a
11	RAD21	chr1:61815757-61815966	HepG2	liver:	n/a	n/a
12	CTCF	chr1:61815780-61815930	RPTEC	kidney:	n/a	n/a
13	CTCF	chr1:61815720-61815870	HVMF	connective:	n/a	n/a
14	RAD21	chr1:61815733-61815941	GM12878	blood:	n/a	n/a
15	RAD21	chr1:61815785-61815944	GM12878	blood:	n/a	n/a
16	CTCF	chr1:61815783-61815964	K562	blood:	n/a	n/a
17	CTCF	chr1:61815720-61815870	NHLF	lung:	n/a	n/a
18	CTCF	chr1:61815780-61815930	K562	blood:	n/a	n/a
19	CTCF	chr1:61815722-61816042	GM12878	blood:	n/a	n/a
20	RAD21	chr1:61815662-61816008	HepG2	liver:	n/a	n/a
21	RAD21	chr1:61815711-61816006	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr1:61815740-61815890	HMEC	breast:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:61444516..61445093-chr1:61815402..61816344,2	MCF-7	breast:
2	chr1:61815681..61817818-chr1:61903758..61906179,2	K562	blood:
3	chr1:61813440..61817104-chr1:61817540..61820998,4	K562	blood:

No data

Variant related genes	Relation type
NFIA	TF binding region
ENSG00000162599	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1041674	0.81[JPT][hapmap]
rs1125777	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap]
rs2024789	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs2782540	0.86[JPT][hapmap]
rs2806435	0.81[JPT][hapmap]
rs2806442	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs41453448	0.86[YRI][hapmap]
rs6691768	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs7521242	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7556462	1.00[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap]
rs9436636	0.83[MEX][hapmap]

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	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
2	nsv1006142	chr1:61696142-62119763	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv534980	chr1:61696142-62119763	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv916868	chr1:61700430-62119762	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1001052	chr1:61702011-62090670	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv817402	chr1:61703965-62119762	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1010797	chr1:61703966-62125970	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv530494	chr1:61723918-62084045	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv1014023	chr1:61788310-61859074	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv534981	chr1:61788310-61859074	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Bipolar disorder	22925353	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs41350144	MYSM1	cis	parietal	SCAN
rs41350144	RPS25	trans	parietal	SCAN
rs41350144	MYSM1	cis	cerebellum	SCAN
rs41350144	PRSS21	trans	lymphoblastoid	seeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61801000-61818600	Weak transcription	K562	blood
2	chr1:61801200-61824600	Weak transcription	Gastric	stomach
3	chr1:61803000-61816200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:61804400-61818200	Weak transcription	Fetal Brain Male	brain
5	chr1:61804400-61818400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:61804400-61818400	Weak transcription	Hela-S3	cervix
7	chr1:61804400-61851400	Weak transcription	Small Intestine	intestine
8	chr1:61804400-61854600	Weak transcription	Placenta	Placenta
9	chr1:61804600-61818200	Weak transcription	Brain Angular Gyrus	brain
10	chr1:61804800-61822800	Weak transcription	Fetal Stomach	stomach
11	chr1:61805000-61818200	Weak transcription	A549	lung
12	chr1:61805000-61818400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr1:61805600-61817600	Weak transcription	HUVEC	blood vessel
14	chr1:61805800-61818000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:61805800-61818200	Weak transcription	Esophagus	oesophagus
16	chr1:61805800-61818600	Weak transcription	Lung	lung
17	chr1:61805800-61848800	Weak transcription	Pancreas	Pancrea
18	chr1:61809400-61818400	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:61810000-61818800	Weak transcription	Fetal Brain Female	brain
20	chr1:61810000-61822600	Weak transcription	Fetal Kidney	kidney
21	chr1:61810200-61824600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:61810200-61827600	Weak transcription	Brain Germinal Matrix	brain
23	chr1:61810400-61818200	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:61810400-61818600	Weak transcription	Aorta	Aorta
25	chr1:61810400-61824200	Weak transcription	Fetal Intestine Small	intestine
26	chr1:61810400-61828000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:61810600-61816000	Weak transcription	HepG2	liver
28	chr1:61810600-61818200	Weak transcription	Fetal Heart	heart
29	chr1:61810600-61818200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:61810600-61824400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:61810600-61828000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:61810600-61831600	Weak transcription	Stomach Mucosa	stomach
33	chr1:61810800-61824400	Weak transcription	Brain Anterior Caudate	brain
34	chr1:61810800-61827800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:61811000-61822400	Weak transcription	Colonic Mucosa	Colon
36	chr1:61811200-61816600	Strong transcription	Liver	Liver
37	chr1:61811400-61818400	Weak transcription	Ovary	ovary
38	chr1:61811600-61818200	Weak transcription	Left Ventricle	heart
39	chr1:61812400-61819000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr1:61813000-61818000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:61813800-61818400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:61813800-61829800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:61814000-61818200	Weak transcription	Right Atrium	heart
44	chr1:61814000-61818400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr1:61814000-61848800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:61814200-61818400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:61814200-61823600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:61814600-61817800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr1:61814600-61818200	Weak transcription	Adipose Nuclei	Adipose
50	chr1:61814600-61818200	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links