Variant report

Variant	rs1374157
Chromosome Location	chr2:151070216-151070217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:151021749..151023909-chr2:151069571..151071445,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10170246	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10174836	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10184785	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10190277	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10195650	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10207680	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1031212	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1031213	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1031214	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1031215	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1031216	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10930038	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1155072	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11682154	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11687868	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11694747	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11886061	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11886070	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12692632	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12692633	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12692644	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12986816	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12996112	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13024074	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13028397	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13419478	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1348741	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2376603	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4260269	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4283445	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4295034	0.89[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4296450	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4318407	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4434022	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4435478	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4461280	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4464296	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4481007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4560135	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4597551	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4597552	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4600677	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4667341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4667343	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62170020	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432680	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6432682	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6432683	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432700	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6650776	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6733918	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7422660	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7557353	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7564853	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7566441	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7569176	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7575612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7580941	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7581265	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7581723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7586530	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7592745	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7600792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604483	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9678528	0.82[ASN][1000 genomes]
rs974902	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv995119	chr2:150556150-151294696	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1001838	chr2:150819672-151745876	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv535980	chr2:150819672-151745876	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv469524	chr2:150927500-151076920	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv834412	chr2:151014270-151116638	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1374157	MLH1	trans	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151063800-151071400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:151065600-151070800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:151066000-151071000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr2:151066000-151071000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:151066000-151071200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr2:151066000-151071200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:151066200-151071000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:151066400-151072800	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:151067000-151070400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:151067600-151071400	Weak transcription	NHLF	lung
11	chr2:151068400-151070400	Enhancers	Fetal Muscle Leg	muscle
12	chr2:151068800-151070600	Enhancers	Fetal Intestine Small	intestine
13	chr2:151068800-151071200	Enhancers	Fetal Intestine Large	intestine
14	chr2:151069000-151070600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:151069000-151073400	Enhancers	Stomach Mucosa	stomach
16	chr2:151069400-151070400	Weak transcription	Ovary	ovary
17	chr2:151069400-151071800	Weak transcription	Small Intestine	intestine
18	chr2:151069600-151070800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:151069600-151071000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:151069600-151071000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr2:151069600-151071000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:151069600-151071200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:151069600-151071200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:151069600-151071400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:151069800-151071000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:151070000-151071200	Weak transcription	Fetal Kidney	kidney
27	chr2:151070000-151071200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:151070200-151070600	Weak transcription	Fetal Lung	lung
29	chr2:151070200-151071000	Enhancers	A549	lung
30	chr2:151070200-151071000	Enhancers	Dnd41	blood

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