Variant report

Variant	rs6978504
Chromosome Location	chr7:26695880-26695881
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	chr7:26692789..26695247-chr7:26695644..26699450,4	MCF-7	breast:
2	chr7:26694010..26696341-chr7:27199658..27201244,2	K562	blood:

Extended variants
information (count: 176 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:170)

rs_ID	r²[population]
rs10085721	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10227140	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10227231	1.00[CHB][hapmap]
rs10227673	1.00[CHB][hapmap]
rs10227898	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs10231161	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs1023712	0.93[EUR][1000 genomes]
rs10239608	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10242572	1.00[CHB][hapmap]
rs10256250	1.00[CHB][hapmap]
rs10256561	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10256799	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs10261915	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10267950	1.00[CHB][hapmap]
rs10269731	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10270187	1.00[CHB][hapmap]
rs10272190	1.00[CHB][hapmap]
rs10272457	1.00[CHB][hapmap]
rs10273468	1.00[CHB][hapmap]
rs10276471	1.00[CHB][hapmap]
rs10281261	1.00[CHB][hapmap]
rs1030648	0.93[EUR][1000 genomes]
rs10486478	0.86[CHB][hapmap]
rs10486483	1.00[CHB][hapmap]
rs10951145	0.88[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10951146	0.93[EUR][1000 genomes]
rs10951147	0.93[EUR][1000 genomes]
rs10951148	0.92[EUR][1000 genomes]
rs10951149	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1123156	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs1123157	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1123158	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs11770043	1.00[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs11772673	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11773029	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs11977233	0.93[EUR][1000 genomes]
rs11980739	0.91[EUR][1000 genomes]
rs12532796	1.00[CHB][hapmap]
rs12534899	1.00[CHB][hapmap]
rs12535784	1.00[CHB][hapmap]
rs12536560	1.00[CHB][hapmap]
rs12537323	1.00[CHB][hapmap]
rs12668948	0.86[ASN][1000 genomes]
rs12700755	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs12700758	0.80[ASN][1000 genomes]
rs12700759	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12700761	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs13186	1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13229947	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs13234201	0.90[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs13234336	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1327988	1.00[CHB][hapmap]
rs1327989	1.00[CHB][hapmap]
rs13438513	1.00[CHB][hapmap]
rs13438514	1.00[CHB][hapmap]
rs1468203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs1548478	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs1548479	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs1548481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs17315775	1.00[CHB][hapmap]
rs17315929	1.00[CHB][hapmap]
rs17372780	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs1859101	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2015543	0.82[ASN][1000 genomes]
rs2015649	0.91[EUR][1000 genomes]
rs2023819	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2030136	1.00[CHB][hapmap]
rs2031811	1.00[CHB][hapmap]
rs2082365	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2106905	1.00[CHB][hapmap]
rs212837	0.80[EUR][1000 genomes]
rs212840	0.83[ASN][1000 genomes]
rs212842	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs212844	0.86[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs212846	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs212847	1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs212849	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs212850	1.00[CHB][hapmap]
rs212852	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs212853	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs212855	0.86[ASN][1000 genomes]
rs212857	1.00[CHB][hapmap]
rs212858	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2189016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs2189017	1.00[CHB][hapmap]
rs2189019	1.00[CHB][hapmap]
rs2237328	0.89[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2282906	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2299102	1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2391360	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs3757654	1.00[CHB][hapmap]
rs3801810	1.00[CHB][hapmap]
rs3801812	1.00[CHB][hapmap]
rs3801813	1.00[CHB][hapmap]
rs3801814	1.00[CHB][hapmap]
rs3801815	1.00[CHB][hapmap]
rs3801816	1.00[CHB][hapmap]
rs3801819	1.00[CHB][hapmap]
rs3801820	1.00[CHB][hapmap]
rs3801821	1.00[CHB][hapmap]
rs3801825	1.00[CHB][hapmap]
rs3801827	1.00[CHB][hapmap]
rs3801828	1.00[CHB][hapmap]
rs3801830	1.00[CHB][hapmap]
rs3801840	1.00[CHB][hapmap]
rs3801842	1.00[CHB][hapmap]
rs3801843	1.00[CHB][hapmap]
rs3801844	1.00[CHB][hapmap]
rs3801846	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs3801848	1.00[CHB][hapmap]
rs3801850	1.00[CHB][hapmap]
rs3801853	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs3801857	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs3801860	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs3801864	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs3823932	1.00[CHB][hapmap]
rs3823933	1.00[CHB][hapmap]
rs3823934	1.00[CHB][hapmap]
rs3823936	1.00[CHB][hapmap]
rs4719877	1.00[CHB][hapmap]
rs4719879	0.80[ASN][1000 genomes]
rs4722630	1.00[CHB][hapmap]
rs4722631	1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4722633	0.82[ASN][1000 genomes]
rs5012512	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs55649724	0.93[EUR][1000 genomes]
rs55959127	0.92[EUR][1000 genomes]
rs56374720	0.91[EUR][1000 genomes]
rs58988613	0.83[ASN][1000 genomes]
rs6461961	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs6461962	1.00[CHB][hapmap]
rs6461963	1.00[CHB][hapmap]
rs6461964	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6461965	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6461970	0.91[EUR][1000 genomes]
rs6461971	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6461979	1.00[CHB][hapmap]
rs6948657	1.00[CHB][hapmap]
rs6951065	1.00[CHB][hapmap]
rs6964094	1.00[CHB][hapmap]
rs6964817	1.00[CHB][hapmap]
rs6970591	0.80[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6971397	1.00[CHB][hapmap]
rs6972378	1.00[CHB][hapmap]
rs6973237	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs727449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs727450	0.89[CHB][hapmap]
rs73061889	0.93[EUR][1000 genomes]
rs73063604	0.93[EUR][1000 genomes]
rs7457076	1.00[CHB][hapmap]
rs763616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs7782621	0.93[EUR][1000 genomes]
rs7785832	1.00[CHB][hapmap]
rs7788165	0.86[ASN][1000 genomes]
rs7791513	1.00[CHB][hapmap]
rs7795074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes]
rs7799888	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7802688	0.95[EUR][1000 genomes]
rs7802852	0.80[ASN][1000 genomes]
rs7803699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs7804356	1.00[CHB][hapmap]
rs7805766	1.00[CHB][hapmap]
rs7807640	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs7810109	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs7810127	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7811764	0.86[ASN][1000 genomes]
rs891876	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs9648019	0.93[EUR][1000 genomes]
rs9648020	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs989250	1.00[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers 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	25 gene(s)	inside rSNPs	diseases
3	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
4	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	nsv830929	chr7:26587888-26749735	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1020378	chr7:26679880-26733872	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6978504	SKAP2	cis	Whole Blood	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26678800-26715400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:26679400-26710000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr7:26680400-26704400	Weak transcription	Primary B cells from cord blood	blood
4	chr7:26685600-26704400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr7:26686400-26701600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr7:26688800-26704400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:26692000-26697400	Enhancers	Brain Germinal Matrix	brain
8	chr7:26692200-26697000	Enhancers	Fetal Brain Male	brain
9	chr7:26692800-26696800	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr7:26692800-26697000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr7:26693000-26696000	Enhancers	Brain Substantia Nigra	brain
12	chr7:26693000-26696200	Enhancers	Fetal Heart	heart
13	chr7:26693000-26697000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr7:26693000-26697000	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr7:26693400-26697000	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr7:26693600-26696800	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr7:26694200-26704000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr7:26694600-26696800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:26694600-26697000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr7:26694600-26697800	Enhancers	H9 Cell Line	embryonic stem cell
21	chr7:26695000-26696800	Enhancers	Fetal Kidney	kidney
22	chr7:26695200-26696000	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr7:26695200-26697000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr7:26695200-26697600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:26695400-26696000	Bivalent Enhancer	Fetal Lung	lung
26	chr7:26695400-26697400	Enhancers	H1 Cell Line	embryonic stem cell
27	chr7:26695400-26697800	Enhancers	Fetal Stomach	stomach
28	chr7:26695600-26697000	Enhancers	Fetal Brain Female	brain
29	chr7:26695600-26698400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr7:26695800-26696200	Weak transcription	Placenta	Placenta
31	chr7:26695800-26696800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:26695800-26697600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr7:26695800-26698200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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