Variant report

Variant	rs13228540
Chromosome Location	chr7:97757075-97757076
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:97756277..97758214-chr7:97760043..97763827,4	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10215577	0.88[EUR][1000 genomes]
rs10216274	0.88[EUR][1000 genomes]
rs10227681	0.88[EUR][1000 genomes]
rs10231625	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10232153	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10241172	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10243993	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10256262	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10261777	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10270280	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10276472	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10282336	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12704966	0.85[EUR][1000 genomes]
rs13221480	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs13228463	1.00[CEU][hapmap]
rs13241860	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13247901	0.88[EUR][1000 genomes]
rs17169317	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17169328	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs28415802	0.88[EUR][1000 genomes]
rs28681561	0.82[EUR][1000 genomes]
rs34228515	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34320281	0.88[EUR][1000 genomes]
rs34353490	0.88[EUR][1000 genomes]
rs35428901	0.82[EUR][1000 genomes]
rs36081491	0.88[EUR][1000 genomes]
rs3735252	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6465655	0.82[EUR][1000 genomes]
rs6958785	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6980318	0.88[EUR][1000 genomes]
rs73404186	0.88[EUR][1000 genomes]
rs7788997	0.88[EUR][1000 genomes]
rs951987	1.00[CEU][hapmap];0.88[EUR][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:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97737200-97762400	Weak transcription	Aorta	Aorta
2	chr7:97737200-97764600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:97737600-97762400	Weak transcription	Small Intestine	intestine
4	chr7:97737800-97759600	Weak transcription	Right Ventricle	heart
5	chr7:97737800-97760800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr7:97737800-97767000	Weak transcription	Fetal Stomach	stomach
7	chr7:97738800-97759200	Weak transcription	Dnd41	blood
8	chr7:97741000-97760400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr7:97741000-97760600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr7:97741200-97767600	Weak transcription	Fetal Brain Male	brain
11	chr7:97742000-97759200	Weak transcription	Fetal Intestine Large	intestine
12	chr7:97743600-97758800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr7:97744000-97757400	Weak transcription	Thymus	Thymus
14	chr7:97744400-97759000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr7:97744800-97760000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:97745000-97759200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr7:97745600-97759800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr7:97745600-97781600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:97746400-97760200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:97746400-97772600	Weak transcription	Fetal Kidney	kidney
21	chr7:97746600-97760200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr7:97746600-97767000	Weak transcription	Esophagus	oesophagus
23	chr7:97746800-97760200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr7:97746800-97761200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr7:97747000-97760400	Weak transcription	Stomach Mucosa	stomach
26	chr7:97748800-97760400	Weak transcription	HUVEC	blood vessel
27	chr7:97749000-97760600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr7:97749400-97760800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr7:97749600-97760800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:97749800-97762400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr7:97750000-97760400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr7:97750200-97760400	Weak transcription	Osteobl	bone
33	chr7:97750400-97757600	Weak transcription	Ovary	ovary
34	chr7:97750600-97759400	Weak transcription	Hela-S3	cervix
35	chr7:97751200-97759800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr7:97751200-97760600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr7:97751400-97761000	Weak transcription	Fetal Thymus	thymus
38	chr7:97751400-97767600	Weak transcription	Brain Germinal Matrix	brain
39	chr7:97752200-97759400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr7:97752200-97759800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr7:97752200-97760600	Weak transcription	K562	blood
42	chr7:97752400-97762200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr7:97752600-97760000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr7:97752600-97761000	Weak transcription	Gastric	stomach
45	chr7:97752600-97780800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr7:97753000-97760200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr7:97753000-97760200	Weak transcription	Brain Hippocampus Middle	brain
48	chr7:97753200-97760800	Weak transcription	Brain Substantia Nigra	brain
49	chr7:97753800-97758600	Weak transcription	Lung	lung
50	chr7:97754000-97759600	Weak transcription	Fetal Intestine Small	intestine

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