Variant report

Variant	rs7029968
Chromosome Location	chr9:96010240-96010241
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95999131..96001082-chr9:96010060..96012180,2	MCF-7	breast:
2	chr9:96006890..96010623-chr9:96016946..96019485,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165238	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10122466	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539670	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs16909000	1.00[CHB][hapmap]
rs16909005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16909016	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1891971	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1891972	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1891973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1936403	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1970622	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744197	0.85[AMR][1000 genomes]
rs4744202	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4744205	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55692827	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55706397	0.85[AMR][1000 genomes]
rs55795421	0.97[ASN][1000 genomes]
rs6479467	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72743431	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72743433	0.85[AMR][1000 genomes]
rs72743435	0.85[AMR][1000 genomes]
rs72743442	0.97[ASN][1000 genomes]
rs72743443	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72743444	0.90[ASN][1000 genomes]
rs72743445	0.90[ASN][1000 genomes]
rs7859604	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7859628	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7871272	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv893583	chr9:95996573-96091688	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv893584	chr9:96002983-96116937	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95995200-96026400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr9:95995600-96030600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:95996400-96011200	Strong transcription	Stomach Smooth Muscle	stomach
4	chr9:95997000-96012400	Weak transcription	Fetal Kidney	kidney
5	chr9:95997600-96012400	Weak transcription	Fetal Brain Male	brain
6	chr9:96000600-96010400	Weak transcription	Fetal Thymus	thymus
7	chr9:96001800-96018800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr9:96002400-96010600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:96002600-96016400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr9:96003600-96010600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:96003800-96010600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:96005000-96010600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:96005400-96033800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:96005600-96010400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:96005600-96026200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:96005800-96010600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr9:96005800-96010600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:96006200-96010600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:96006200-96015200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr9:96006200-96043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:96006600-96014600	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:96007000-96014800	Weak transcription	Brain Substantia Nigra	brain
23	chr9:96007000-96020400	Weak transcription	Fetal Muscle Leg	muscle
24	chr9:96007400-96010600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:96007400-96015200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr9:96007600-96011000	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr9:96007800-96010400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:96007800-96012600	Strong transcription	Fetal Brain Female	brain
29	chr9:96008000-96014400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr9:96008000-96030200	Strong transcription	Fetal Intestine Small	intestine
31	chr9:96008000-96030400	Strong transcription	Fetal Intestine Large	intestine
32	chr9:96008200-96010600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr9:96008200-96011200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr9:96008200-96026600	Weak transcription	Spleen	Spleen
35	chr9:96008200-96027600	Weak transcription	Right Atrium	heart
36	chr9:96008400-96010400	Weak transcription	Psoas Muscle	Psoas
37	chr9:96008400-96014400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:96008400-96014600	Weak transcription	Hela-S3	cervix
39	chr9:96008400-96016600	Weak transcription	Gastric	stomach
40	chr9:96008600-96011000	Strong transcription	Fetal Stomach	stomach
41	chr9:96008600-96013000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr9:96008600-96013000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr9:96008800-96010600	Strong transcription	Colonic Mucosa	Colon
44	chr9:96008800-96011000	Enhancers	Brain Hippocampus Middle	brain
45	chr9:96008800-96017200	Weak transcription	Brain Angular Gyrus	brain
46	chr9:96008800-96026200	Weak transcription	Placenta	Placenta
47	chr9:96009000-96010400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr9:96009000-96014200	Weak transcription	Fetal Heart	heart
49	chr9:96009200-96010800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr9:96009200-96010800	Strong transcription	Brain Germinal Matrix	brain

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