Variant report

Variant	rs7042968
Chromosome Location	chr9:116287351-116287352
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	chr9:116285543..116288379-chr9:116298263..116300246,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138835	Chromatin interaction

Extended variants
information (count: 194 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:189)

rs_ID	r²[population]
rs10125960	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10217237	0.90[AFR][1000 genomes]
rs10217750	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10217756	0.90[AFR][1000 genomes]
rs10481640	0.90[AFR][1000 genomes]
rs10481676	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10481677	0.94[AFR][1000 genomes]
rs10981793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981794	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs10981803	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs10981807	0.97[AFR][1000 genomes]
rs10981808	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs10981814	0.95[YRI][hapmap];0.97[AFR][1000 genomes]
rs10981815	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10981816	0.95[YRI][hapmap];0.97[AFR][1000 genomes]
rs10981817	0.95[YRI][hapmap];0.97[AFR][1000 genomes]
rs10981819	0.94[YRI][hapmap];0.96[AFR][1000 genomes]
rs10981820	0.97[AFR][1000 genomes]
rs10981821	0.97[AFR][1000 genomes]
rs10981825	0.96[AFR][1000 genomes]
rs10981826	0.96[AFR][1000 genomes]
rs10981827	0.96[AFR][1000 genomes]
rs10981830	0.84[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10981832	0.87[AFR][1000 genomes]
rs10981834	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981835	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12335991	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs12336719	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs12337340	0.94[YRI][hapmap];0.93[AFR][1000 genomes]
rs12338221	0.89[AFR][1000 genomes]
rs12338588	0.89[AFR][1000 genomes]
rs12338697	0.94[YRI][hapmap];0.93[AFR][1000 genomes]
rs12338701	0.95[YRI][hapmap];0.93[AFR][1000 genomes]
rs12338788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12339493	0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs12339617	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs12339851	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs12340996	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs12341332	0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs12342508	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs12342699	0.89[AFR][1000 genomes]
rs12343129	0.94[YRI][hapmap];0.89[AFR][1000 genomes]
rs12343141	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs12344334	0.96[AFR][1000 genomes]
rs12344578	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs12344964	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs12345524	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs12346076	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs12346087	0.95[YRI][hapmap];0.92[AFR][1000 genomes]
rs12346939	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs12347382	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12347895	0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs12351728	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17525042	1.00[ASN][1000 genomes]
rs17553698	1.00[ASN][1000 genomes]
rs1890992	0.94[YRI][hapmap];0.96[AFR][1000 genomes]
rs2050865	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2050866	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs28694002	0.97[AFR][1000 genomes]
rs28709996	0.90[AFR][1000 genomes]
rs28714985	0.97[AFR][1000 genomes]
rs34106027	1.00[ASN][1000 genomes]
rs34142167	1.00[ASN][1000 genomes]
rs35120599	1.00[ASN][1000 genomes]
rs35270441	0.93[AFR][1000 genomes]
rs35329679	1.00[ASN][1000 genomes]
rs3747813	1.00[CHB][hapmap]
rs3761819	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3810925	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3810926	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3827674	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3983381	0.95[YRI][hapmap];0.96[AFR][1000 genomes]
rs41276809	1.00[ASN][1000 genomes]
rs41301525	0.92[AFR][1000 genomes]
rs41305473	0.92[AFR][1000 genomes]
rs41312200	1.00[ASN][1000 genomes]
rs41316948	1.00[ASN][1000 genomes]
rs4596719	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs4979257	0.94[YRI][hapmap];0.86[AFR][1000 genomes]
rs55676913	0.90[AFR][1000 genomes]
rs55714377	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55777057	0.96[AFR][1000 genomes]
rs55931715	0.96[AFR][1000 genomes]
rs55977108	0.97[AFR][1000 genomes]
rs56155263	0.91[AFR][1000 genomes]
rs56276438	0.96[AFR][1000 genomes]
rs56390346	0.96[AFR][1000 genomes]
rs6478011	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs6478016	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs6478017	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs6478022	0.95[YRI][hapmap];0.96[AFR][1000 genomes]
rs6478023	0.95[YRI][hapmap];0.96[AFR][1000 genomes]
rs7018783	0.95[YRI][hapmap];0.97[AFR][1000 genomes]
rs7020623	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7021491	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7023661	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7024445	0.95[YRI][hapmap];0.96[AFR][1000 genomes]
rs7024612	0.94[YRI][hapmap];0.96[AFR][1000 genomes]
rs7024996	0.95[YRI][hapmap];0.94[AFR][1000 genomes]
rs7025170	0.96[AFR][1000 genomes]
rs7025745	0.97[AFR][1000 genomes]
rs7026568	0.93[AFR][1000 genomes]
rs7026656	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs7027024	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs7027340	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7028327	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7029685	0.97[AFR][1000 genomes]
rs7033679	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7037441	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs7037761	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7040031	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7040635	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7041833	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs7042290	0.90[AFR][1000 genomes]
rs7042695	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs7043140	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs7045347	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7046202	0.90[AFR][1000 genomes]
rs7046427	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs7047062	0.95[YRI][hapmap];0.92[AFR][1000 genomes]
rs7048208	0.81[AFR][1000 genomes]
rs7049221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72760096	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72761903	0.89[AFR][1000 genomes]
rs72761905	0.90[AFR][1000 genomes]
rs72761906	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72761963	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72761964	0.90[AFR][1000 genomes]
rs72761965	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72761966	0.87[AFR][1000 genomes]
rs72761969	0.90[AFR][1000 genomes]
rs72761971	0.90[AFR][1000 genomes]
rs72761973	0.90[AFR][1000 genomes]
rs72761978	0.90[AFR][1000 genomes]
rs72761987	0.93[AFR][1000 genomes]
rs72761992	0.97[AFR][1000 genomes]
rs72761994	0.97[AFR][1000 genomes]
rs72761999	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72762002	0.97[AFR][1000 genomes]
rs72763803	0.93[AFR][1000 genomes]
rs72763804	0.97[AFR][1000 genomes]
rs72763826	0.92[AFR][1000 genomes]
rs72763828	0.87[AFR][1000 genomes]
rs72763831	0.92[AFR][1000 genomes]
rs72763841	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72763842	0.92[AFR][1000 genomes]
rs72763843	0.83[AFR][1000 genomes]
rs72763846	0.90[AFR][1000 genomes]
rs72763856	0.81[EUR][1000 genomes]
rs72763857	0.84[EUR][1000 genomes]
rs7848203	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7849841	0.90[AFR][1000 genomes]
rs7851718	0.94[YRI][hapmap];0.97[AFR][1000 genomes]
rs7851937	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7852118	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7853373	0.97[AFR][1000 genomes]
rs7853792	0.90[YRI][hapmap];0.96[AFR][1000 genomes]
rs7854197	0.95[YRI][hapmap];0.97[AFR][1000 genomes]
rs7854524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7855325	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs7855434	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7856689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857217	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7857943	0.95[YRI][hapmap];0.92[AFR][1000 genomes]
rs7860673	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7861248	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7863159	0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs7864467	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7864645	0.90[AFR][1000 genomes]
rs7864816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7867353	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs7870142	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7870227	0.94[YRI][hapmap];0.97[AFR][1000 genomes]
rs7870265	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7870451	0.95[YRI][hapmap]
rs7870912	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7871186	0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs7872084	0.83[AFR][1000 genomes]
rs7872283	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs883025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs884898	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs884899	0.93[AFR][1000 genomes]
rs9299215	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs944345	0.95[YRI][hapmap];0.96[AFR][1000 genomes]
rs944346	0.95[YRI][hapmap];0.96[AFR][1000 genomes]
rs9657641	0.95[YRI][hapmap];0.92[AFR][1000 genomes]
rs9657658	0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs9657659	0.95[YRI][hapmap];0.92[AFR][1000 genomes]
rs9785299	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv466508	chr9:116244982-116362738	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv615215	chr9:116244982-116362738	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116264000-116291200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:116264800-116298400	Weak transcription	Brain Germinal Matrix	brain
3	chr9:116269000-116288600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:116269400-116288200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr9:116269400-116303000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr9:116269600-116298400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr9:116270400-116289200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:116270400-116290600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr9:116277200-116298600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:116277600-116298600	Weak transcription	Fetal Brain Female	brain
11	chr9:116281600-116288000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:116282000-116287800	Enhancers	HSMMtube	muscle
13	chr9:116282200-116288400	Weak transcription	Fetal Kidney	kidney
14	chr9:116282800-116295600	Strong transcription	HepG2	liver
15	chr9:116283400-116287400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr9:116283400-116288000	Genic enhancers	Fetal Intestine Small	intestine
17	chr9:116283800-116287400	Enhancers	Colon Smooth Muscle	Colon
18	chr9:116284400-116290600	Enhancers	Fetal Lung	lung
19	chr9:116284600-116288400	Enhancers	Psoas Muscle	Psoas
20	chr9:116284600-116289400	Genic enhancers	Spleen	Spleen
21	chr9:116284600-116290200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr9:116284600-116290800	Genic enhancers	Fetal Stomach	stomach
23	chr9:116284800-116287400	Enhancers	Esophagus	oesophagus
24	chr9:116284800-116287400	Genic enhancers	Lung	lung
25	chr9:116284800-116287600	Enhancers	Ovary	ovary
26	chr9:116284800-116289600	Enhancers	Right Atrium	heart
27	chr9:116284800-116290400	Enhancers	Fetal Heart	heart
28	chr9:116285000-116287400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:116285000-116287600	Flanking Active TSS	Colonic Mucosa	Colon
30	chr9:116285200-116287600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
31	chr9:116285200-116288200	Genic enhancers	Right Ventricle	heart
32	chr9:116285200-116290600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:116285400-116287400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:116285400-116287600	Genic enhancers	Fetal Intestine Large	intestine
35	chr9:116285600-116288200	Enhancers	Fetal Muscle Leg	muscle
36	chr9:116285800-116287800	Genic enhancers	Liver	Liver
37	chr9:116285800-116288200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:116285800-116288800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr9:116285800-116289000	Enhancers	Adipose Nuclei	Adipose
40	chr9:116285800-116289000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
41	chr9:116285800-116290400	Weak transcription	A549	lung
42	chr9:116286000-116288200	Enhancers	Fetal Thymus	thymus
43	chr9:116286000-116288200	Enhancers	Thymus	Thymus
44	chr9:116286200-116287400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr9:116286200-116288000	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr9:116286200-116288800	Genic enhancers	HUVEC	blood vessel
47	chr9:116286200-116290400	Enhancers	Brain Hippocampus Middle	brain
48	chr9:116286200-116291000	Enhancers	Stomach Mucosa	stomach
49	chr9:116286400-116287400	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr9:116286400-116287400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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