Variant report

Variant	rs1250171
Chromosome Location	chr18:12027028-12027029
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	chr18:12026979-12027311	H1-hESC	embryonic stem cell:	n/a	n/a
2	ESR1	chr18:12026840-12027458	ECC-1	luminal epithelium:	n/a	n/a
3	FOS	chr18:12026997-12027401	MCF10A-Er-Src	breast:	n/a	chr18:12027247-12027255 chr18:12027044-12027054 chr18:12027245-12027257
4	MYC	chr18:12026805-12027391	MCF10A-Er-Src	breast:	n/a	chr18:12026966-12026975
5	ESR1	chr18:12026833-12027405	ECC-1	luminal epithelium:	n/a	n/a
6	NFIC	chr18:12026628-12027568	ECC-1	luminal epithelium:	n/a	chr18:12026902-12026930
7	POLR2A	chr18:12026522-12027424	Hela-S3	cervix:	n/a	n/a
8	EP300	chr18:12026476-12027562	ECC-1	luminal epithelium:	n/a	n/a
9	ESR1	chr18:12026790-12027476	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr18:12026603-12027124	Hela-S3	cervix:	n/a	n/a
11	NFIC	chr18:12026617-12027547	ECC-1	luminal epithelium:	n/a	chr18:12026902-12026930
12	TCF12	chr18:12026482-12027567	ECC-1	luminal epithelium:	n/a	chr18:12026925-12026932 chr18:12027133-12027140 chr18:12027352-12027359
13	MAX	chr18:12027006-12027434	ECC-1	luminal epithelium:	n/a	n/a
14	TCF12	chr18:12026385-12027562	ECC-1	luminal epithelium:	n/a	chr18:12026925-12026932 chr18:12027133-12027140 chr18:12027352-12027359

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12025555..12027976-chr18:12028619..12030454,2	K562	blood:
2	chr18:12015892..12018624-chr18:12025559..12027409,2	K562	blood:

Variant related genes	Relation type
IMPA2	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1036903	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1036904	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1530368	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1662607	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1662612	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1662613	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1964436	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2075826	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2849416	0.81[CHD][hapmap]
rs2851915	1.00[ASW][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.90[LWK][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2851916	0.83[ASN][1000 genomes]
rs2851928	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2851930	0.81[ASN][1000 genomes]
rs4797615	0.81[CHD][hapmap]
rs56076781	0.87[ASN][1000 genomes]
rs583965	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs594235	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs596081	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs596142	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs597072	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs597094	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs597147	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs597965	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs597973	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs598005	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs609104	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs609588	0.87[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs613993	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs627448	0.93[ASN][1000 genomes]
rs627492	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs640088	0.83[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6505710	0.81[CHD][hapmap]
rs655840	0.87[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs656193	0.94[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs674758	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs687869	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7236715	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic 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	35 gene(s)	inside rSNPs	diseases
4	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv909388	chr18:11987988-12141372	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv909389	chr18:11987988-12141625	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv909390	chr18:11987988-12155371	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv528699	chr18:11989416-12029857	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv909391	chr18:11989416-12146408	Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv909392	chr18:11989416-12146698	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	nsv909393	chr18:12001258-12155371	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv909394	chr18:12017343-12141372	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1250171	CLC	trans	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11982600-12028600	Weak transcription	Small Intestine	intestine
2	chr18:11996600-12035000	Weak transcription	Primary T cells from cord blood	blood
3	chr18:11996800-12034400	Weak transcription	Primary B cells from cord blood	blood
4	chr18:11997000-12034400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr18:11998400-12034000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr18:11998800-12029400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr18:11999000-12034000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr18:11999000-12035400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr18:11999200-12035800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr18:12002000-12028400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr18:12015000-12028400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr18:12015200-12028400	Weak transcription	Thymus	Thymus
13	chr18:12015600-12028000	Weak transcription	Colonic Mucosa	Colon
14	chr18:12015600-12028200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr18:12015800-12030400	Strong transcription	Fetal Stomach	stomach
16	chr18:12016000-12028000	Weak transcription	Spleen	Spleen
17	chr18:12016000-12032400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr18:12016000-12032400	Weak transcription	HSMM	muscle
19	chr18:12016200-12038000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr18:12016400-12028400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr18:12016400-12030200	Weak transcription	Fetal Kidney	kidney
22	chr18:12016400-12032600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr18:12016600-12032400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr18:12017000-12028400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr18:12017400-12028200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr18:12017400-12028200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr18:12017600-12028000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr18:12017600-12031800	Weak transcription	Osteobl	bone
29	chr18:12017600-12038400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr18:12017800-12028000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr18:12018600-12027400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr18:12018600-12028000	Weak transcription	Aorta	Aorta
33	chr18:12018800-12027800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr18:12020000-12028400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr18:12021200-12029800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr18:12021800-12028000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr18:12022000-12028000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr18:12022200-12028200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr18:12022600-12029000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr18:12023000-12033400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr18:12023200-12033600	Strong transcription	Fetal Intestine Small	intestine
42	chr18:12023400-12028200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr18:12023400-12033000	Weak transcription	HSMMtube	muscle
44	chr18:12023600-12027200	Weak transcription	Gastric	stomach
45	chr18:12023600-12027800	Weak transcription	Fetal Lung	lung
46	chr18:12023600-12028600	Weak transcription	Ovary	ovary
47	chr18:12023600-12029800	Weak transcription	A549	lung
48	chr18:12023800-12027200	Weak transcription	Adipose Nuclei	Adipose
49	chr18:12023800-12028000	Weak transcription	Lung	lung
50	chr18:12023800-12028200	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links