Variant report

Variant	rs12155419
Chromosome Location	chr7:110162264-110162265
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:109858826..109860608-chr7:110161184..110163464,2	MCF-7	breast:
2	chr7:110158309..110160168-chr7:110161330..110163385,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10808165	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12154592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12155135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12155486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12666715	0.88[AFR][1000 genomes]
rs12668969	0.90[ASN][1000 genomes]
rs12672609	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12705696	0.88[AFR][1000 genomes]
rs12705699	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12705702	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12705704	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12705705	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12705706	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705707	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12705712	0.94[AFR][1000 genomes]
rs12705714	0.88[AFR][1000 genomes]
rs13221425	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13237799	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13239034	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13239340	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13246981	0.88[ASN][1000 genomes]
rs1396170	0.88[AFR][1000 genomes]
rs1396172	0.88[AFR][1000 genomes]
rs1508182	0.88[AFR][1000 genomes]
rs1508187	0.88[AFR][1000 genomes]
rs1508192	0.83[AMR][1000 genomes]
rs1508199	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1508202	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1532975	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1848384	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1876502	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2940367	0.81[ASN][1000 genomes]
rs35003955	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35651604	0.86[ASN][1000 genomes]
rs35706071	0.88[AFR][1000 genomes]
rs4146060	0.94[AFR][1000 genomes]
rs4730433	0.87[ASN][1000 genomes]
rs6975627	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71542790	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7455199	0.94[AFR][1000 genomes]
rs7778205	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7790198	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7796974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7800391	0.88[AFR][1000 genomes]
rs7803158	1.00[ASW][hapmap]
rs953727	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs953729	0.89[CEU][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023428	chr7:109451842-110185072	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1016758	chr7:109834827-110549197	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv539059	chr7:109834827-110549197	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1028635	chr7:109896582-110417137	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv539060	chr7:109896582-110417137	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv427800	chr7:109949176-110257457	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1023596	chr7:109984459-110708071	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv539061	chr7:109984459-110708071	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv888966	chr7:110127814-110183622	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv888967	chr7:110133558-110183622	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv888968	chr7:110144415-110204292	Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv888969	chr7:110147378-110334465	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv1032498	chr7:110151471-110508283	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1018254	chr7:110152875-110195366	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv1028190	chr7:110152875-110197412	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv1032748	chr7:110157227-110195366	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv1021693	chr7:110157227-110197412	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv1022043	chr7:110158246-110191057	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv5897	chr7:110160821-110208234	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12155419	DLD	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:110155400-110162600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:110159800-110170400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr7:110160200-110163000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:110160800-110163600	Enhancers	HepG2	liver
5	chr7:110160800-110163800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:110161200-110162600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr7:110161200-110163200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr7:110161400-110163400	Enhancers	Fetal Intestine Large	intestine
9	chr7:110161600-110162800	Enhancers	Brain Hippocampus Middle	brain
10	chr7:110161600-110163200	Enhancers	Pancreas	Pancrea
11	chr7:110161600-110163400	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr7:110161600-110163600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:110161600-110163800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:110161800-110163200	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr7:110161800-110163400	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr7:110161800-110163400	Enhancers	Fetal Intestine Small	intestine
17	chr7:110161800-110163600	Enhancers	Fetal Heart	heart
18	chr7:110162000-110162400	Enhancers	Brain Substantia Nigra	brain
19	chr7:110162000-110163000	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr7:110162200-110162600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr7:110162200-110162800	Flanking Active TSS	A549	lung
22	chr7:110162200-110163000	Enhancers	Dnd41	blood
23	chr7:110162200-110163600	Enhancers	Liver	Liver
24	chr7:110162200-110164400	Enhancers	Fetal Kidney	kidney

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