Variant report

Variant	rs7738141
Chromosome Location	chr6:25088861-25088862
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr6:25088394-25089175	HUVEC	blood vessel:	n/a	chr6:25088961-25088970
2	STAT3	chr6:25088676-25089147	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr6:25088646-25089171	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr6:25088735-25089228	HUVEC	blood vessel:	n/a	chr6:25088961-25088970 chr6:25088965-25088976
5	POLR2A	chr6:25088788-25089065	SK-N-SH	brain:	n/a	n/a
6	MYC	chr6:25088794-25089097	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr6:25088746-25089131	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr6:25088794-25089077	MCF10A-Er-Src	breast:	n/a	chr6:25088961-25088970 chr6:25088965-25088976
9	POLR2A	chr6:25088754-25089220	HUVEC	blood vessel:	n/a	n/a
10	SPI1	chr6:25088677-25089044	HL-60	blood:	n/a	chr6:25088957-25088970
11	POLR2A	chr6:25088699-25089267	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr6:25088793-25089133	MCF10A-Er-Src	breast:	n/a	chr6:25088961-25088970 chr6:25088965-25088976
13	POLR2A	chr6:25088816-25089011	HUVEC	blood vessel:	n/a	n/a
14	FOSL2	chr6:25088764-25089264	SK-N-SH	brain:	n/a	chr6:25088961-25088970
15	FOS	chr6:25088790-25089131	MCF10A-Er-Src	breast:	n/a	chr6:25088961-25088970 chr6:25088965-25088976
16	EP300	chr6:25088829-25089193	SK-N-SH_RA	brain:	n/a	chr6:25088959-25088968 chr6:25088958-25088972
17	E2F4	chr6:25088760-25089001	MCF10A-Er-Src	breast:	n/a	n/a
18	EP300	chr6:25088776-25089092	SK-N-SH_RA	brain:	n/a	chr6:25088959-25088968 chr6:25088958-25088972

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25084985..25086769-chr6:25088550..25090244,2	MCF-7	breast:

Variant related genes	Relation type
CMAHP	TF binding region
ENSG00000168405	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1002539	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs1002540	0.88[ASN][1000 genomes]
rs1037167	0.88[ASN][1000 genomes]
rs1037168	0.81[CEU][hapmap];0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs11757374	0.85[CHB][hapmap];0.97[CHD][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12665174	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs13203073	0.89[EUR][1000 genomes]
rs13209444	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1447242	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs1562422	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs1562423	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs1597010	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs1597011	0.82[CEU][hapmap]
rs160034	0.88[EUR][1000 genomes]
rs1900551	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs192773	1.00[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs2273671	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs302992	0.88[EUR][1000 genomes]
rs303879	1.00[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs303880	1.00[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs303884	0.88[EUR][1000 genomes]
rs34322558	0.88[EUR][1000 genomes]
rs34693126	0.83[EUR][1000 genomes]
rs36078207	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3792974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792976	0.88[ASN][1000 genomes]
rs3792977	0.88[ASN][1000 genomes]
rs3792978	0.85[CHB][hapmap];0.92[CHD][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs3792982	0.88[ASN][1000 genomes]
rs3792983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812107	0.85[CHB][hapmap];0.92[CHD][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs3812108	0.85[CHB][hapmap];0.97[CHD][hapmap];0.81[MEX][hapmap];0.88[ASN][1000 genomes]
rs3812109	0.85[CEU][hapmap];0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs3828730	0.85[CHB][hapmap];0.92[CHD][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs3828731	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs4711071	1.00[YRI][hapmap]
rs4711073	1.00[YRI][hapmap]
rs4711074	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4711075	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711076	0.84[CHB][hapmap];0.88[ASN][1000 genomes]
rs4712882	0.87[CHD][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs4712884	0.88[ASN][1000 genomes]
rs56108659	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67927735	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6928752	0.85[ASN][1000 genomes]
rs6928763	0.85[CHB][hapmap];0.92[CHD][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs71555176	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72826363	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs895676	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9461098	0.85[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs9467386	0.85[CHB][hapmap];0.92[CHD][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs9467392	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv470806	chr6:25082262-25156197	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv462662	chr6:25084718-25165486	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv601166	chr6:25084718-25165486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7738141	HIST1H4G	cis	cerebellum	SCAN
rs7738141	HIST1H2BI	cis	cerebellum	SCAN
rs7738141	HIST1H1E	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25079400-25093000	Weak transcription	Ovary	ovary
2	chr6:25080400-25098000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:25081200-25092000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:25082200-25094800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:25082600-25105200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:25083800-25089800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:25083800-25093200	Weak transcription	Colonic Mucosa	Colon
8	chr6:25084200-25089800	Weak transcription	Hela-S3	cervix
9	chr6:25084800-25099000	Weak transcription	Fetal Intestine Large	intestine
10	chr6:25084800-25113800	Weak transcription	Gastric	stomach
11	chr6:25085200-25089400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr6:25085200-25108000	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:25085400-25091600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:25086200-25096400	Strong transcription	Thymus	Thymus
15	chr6:25086400-25089800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr6:25086400-25099600	Strong transcription	Placenta	Placenta
17	chr6:25086600-25090000	Strong transcription	Stomach Smooth Muscle	stomach
18	chr6:25086600-25090400	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:25086600-25096600	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr6:25087000-25089000	Weak transcription	Liver	Liver
21	chr6:25087000-25090600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr6:25087000-25093000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:25087000-25105400	Weak transcription	GM12878-XiMat	blood
24	chr6:25087200-25089000	Weak transcription	Spleen	Spleen
25	chr6:25087200-25090200	Genic enhancers	Primary hematopoietic stem cells	blood
26	chr6:25087200-25091400	Weak transcription	Esophagus	oesophagus
27	chr6:25087400-25089400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:25087400-25089600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:25087400-25089600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:25087400-25089800	Weak transcription	Left Ventricle	heart
31	chr6:25087400-25092200	Weak transcription	Primary B cells from cord blood	blood
32	chr6:25087400-25098200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:25087400-25101600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr6:25087400-25113800	Strong transcription	Fetal Thymus	thymus
35	chr6:25087600-25091200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:25087600-25105400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:25087600-25124800	Weak transcription	Small Intestine	intestine
38	chr6:25087800-25089000	Weak transcription	HSMMtube	muscle
39	chr6:25087800-25089400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:25087800-25093000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr6:25087800-25093400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr6:25087800-25097200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr6:25088000-25105800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr6:25088200-25089200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:25088200-25089600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:25088200-25091200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr6:25088400-25089200	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr6:25088400-25090200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:25088400-25090400	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr6:25088400-25096600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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