Variant report

Variant	rs13241860
Chromosome Location	chr7:97742454-97742455
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:97737661..97739310-chr7:97740344..97742596,2	MCF-7	breast:
2	chr7:97739559..97743131-chr7:97746340..97751154,6	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10215577	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10216274	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10227681	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10230846	0.80[ASN][1000 genomes]
rs10231625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10232153	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10241172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10243993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10252338	0.85[AMR][1000 genomes]
rs10256262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10261777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10276472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10282336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10282640	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11980911	0.88[ASW][hapmap]
rs12704966	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12704976	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.82[ASN][1000 genomes]
rs13221415	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13221480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13228463	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13228540	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13247901	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1532381	0.84[ASN][1000 genomes]
rs16869462	0.88[ASW][hapmap];0.83[LWK][hapmap];0.85[YRI][hapmap]
rs17169317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17169328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17169330	0.87[ASN][1000 genomes]
rs28415802	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28681561	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3148	0.84[YRI][hapmap]
rs34228515	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs34320281	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34353490	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35428901	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36081491	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6465655	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958785	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6980318	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73404186	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7788997	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers 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	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1816676	chr7:97676259-97868033	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97737000-97745200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:97737000-97746200	Weak transcription	Spleen	Spleen
3	chr7:97737200-97745600	Weak transcription	Gastric	stomach
4	chr7:97737200-97746200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:97737200-97762400	Weak transcription	Aorta	Aorta
6	chr7:97737200-97764600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr7:97737400-97743400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:97737400-97744400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr7:97737600-97754400	Weak transcription	HSMMtube	muscle
10	chr7:97737600-97762400	Weak transcription	Small Intestine	intestine
11	chr7:97737800-97743600	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr7:97737800-97745600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:97737800-97748600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr7:97737800-97749400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr7:97737800-97751000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr7:97737800-97759600	Weak transcription	Right Ventricle	heart
17	chr7:97737800-97760800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr7:97737800-97767000	Weak transcription	Fetal Stomach	stomach
19	chr7:97738000-97743000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr7:97738000-97746200	Weak transcription	NHEK	skin
21	chr7:97738000-97748400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr7:97738000-97748400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr7:97738000-97751600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr7:97738400-97742800	Weak transcription	Primary B cells from cord blood	blood
25	chr7:97738600-97742800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr7:97738600-97744400	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr7:97738800-97759200	Weak transcription	Dnd41	blood
28	chr7:97739400-97753400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr7:97739600-97746200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr7:97739600-97752400	Weak transcription	Fetal Lung	lung
31	chr7:97739800-97745600	Weak transcription	Ovary	ovary
32	chr7:97739800-97745600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr7:97739800-97746200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr7:97740000-97742800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr7:97740000-97746400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr7:97740200-97745600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr7:97740200-97748000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr7:97740200-97749800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:97740200-97755200	Weak transcription	Fetal Brain Female	brain
40	chr7:97740400-97745600	Weak transcription	Hela-S3	cervix
41	chr7:97740400-97746200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr7:97740400-97746400	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr7:97740600-97742600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr7:97740600-97751600	Weak transcription	Brain Hippocampus Middle	brain
45	chr7:97741000-97743800	Weak transcription	Fetal Intestine Small	intestine
46	chr7:97741000-97745600	Weak transcription	Brain Angular Gyrus	brain
47	chr7:97741000-97745600	Weak transcription	Fetal Heart	heart
48	chr7:97741000-97745600	Weak transcription	A549	lung
49	chr7:97741000-97745800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr7:97741000-97746000	Weak transcription	Duodenum Mucosa	Duodenum

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