Variant report

Variant	rs2237231
Chromosome Location	chr6:26017171-26017172
allele	A/G
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	FOS	chr6:26016925-26017218	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr6:26017083-26017216	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr6:26017030-26017347	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr6:26016961-26017292	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr6:26016918-26018312	HUVEC	blood vessel:	n/a	n/a
6	FOS	chr6:26016867-26017393	MCF10A-Er-Src	breast:	n/a	n/a
7	MYC	chr6:26017047-26018076	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr6:26016551-26018222	H1-hESC	embryonic stem cell:	n/a	n/a
9	ATF2	chr6:26017065-26017919	H1-hESC	embryonic stem cell:	n/a	n/a
10	RCOR1	chr6:26016562-26018786	IMR90	lung:	n/a	n/a
11	POLR2A	chr6:26016538-26018308	H1-hESC	embryonic stem cell:	n/a	n/a
12	TAF7	chr6:26016766-26018365	H1-hESC	embryonic stem cell:	n/a	n/a
13	FOS	chr6:26016903-26017215	MCF10A-Er-Src	breast:	n/a	n/a
14	STAT3	chr6:26017015-26017204	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr6:26016425-26017408	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25991481..25993438-chr6:26015538..26017595,2	MCF-7	breast:
2	chr6:26016695..26019436-chr6:26198057..26199976,2	MCF-7	breast:

Variant related genes	Relation type
HIST1H4A	TF binding region
HIST1H3A	TF binding region
ENSG00000196866	Chromatin interaction
ENSG00000272462	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000197409	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1014795	0.87[AMR][1000 genomes]
rs10946801	0.81[JPT][hapmap]
rs1800708	1.00[ASW][hapmap];0.93[GIH][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap]
rs2050947	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2051542	1.00[ASW][hapmap];0.90[GIH][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap]
rs2230653	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.92[ASN][1000 genomes]
rs3752418	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3830054	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6908263	0.90[GIH][hapmap];0.90[TSI][hapmap]
rs7753826	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9295676	1.00[ASW][hapmap];0.85[MEX][hapmap]
rs9295682	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs933199	1.00[ASW][hapmap];0.94[GIH][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap]
rs9366637	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9379817	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9393682	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9467667	0.86[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv432857	chr6:25957109-26072445	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	451 gene(s)	inside rSNPs	diseases
8	nsv1015627	chr6:25973495-26100483	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
9	nsv538164	chr6:25973495-26100483	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
10	nsv1028456	chr6:25984457-26174993	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
11	nsv538165	chr6:25984457-26174993	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
12	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
13	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
14	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
15	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
16	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2237231	TRIM38	cis	lymphoblastoid	seeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25999200-26017200	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr6:25999400-26017400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr6:26001600-26017600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:26001600-26020600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:26005400-26017200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:26008800-26020600	Weak transcription	Spleen	Spleen
7	chr6:26016200-26017600	Active TSS	Fetal Lung	lung
8	chr6:26016200-26018400	Flanking Active TSS	Fetal Muscle Leg	muscle
9	chr6:26016200-26018600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:26016200-26019800	Active TSS	Fetal Kidney	kidney
11	chr6:26016400-26017400	Flanking Active TSS	Brain Germinal Matrix	brain
12	chr6:26016400-26017400	Flanking Active TSS	NH-A	brain
13	chr6:26016400-26017400	Active TSS	NHLF	lung
14	chr6:26016400-26017600	Active TSS	Right Ventricle	heart
15	chr6:26016400-26017800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:26016400-26017800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:26016400-26017800	Flanking Active TSS	Fetal Intestine Small	intestine
18	chr6:26016400-26018000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:26016400-26018000	Active TSS	Left Ventricle	heart
20	chr6:26016400-26018000	Active TSS	Right Atrium	heart
21	chr6:26016400-26018200	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr6:26016400-26018200	Active TSS	Ovary	ovary
23	chr6:26016400-26018400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:26016400-26018600	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr6:26016600-26017200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:26016600-26017200	Active TSS	Rectal Smooth Muscle	rectum
27	chr6:26016600-26017200	Active TSS	Stomach Smooth Muscle	stomach
28	chr6:26016600-26017400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:26016600-26017600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:26016600-26017600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
31	chr6:26016600-26017800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:26016600-26017800	Flanking Active TSS	NHEK	skin
33	chr6:26016600-26017800	Flanking Active TSS	Osteobl	bone
34	chr6:26016600-26018000	Active TSS	Fetal Heart	heart
35	chr6:26016600-26018000	Flanking Active TSS	HUVEC	blood vessel
36	chr6:26016600-26018200	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr6:26016600-26018200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr6:26016600-26018200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:26016600-26018200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
40	chr6:26016600-26018200	Flanking Active TSS	HMEC	breast
41	chr6:26016600-26018200	Active TSS	NHDF-Ad	bronchial
42	chr6:26016600-26018400	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr6:26016600-26018400	Active TSS	Aorta	Aorta
44	chr6:26016600-26018400	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr6:26016600-26018600	Active TSS	H9 Cell Line	embryonic stem cell
46	chr6:26016800-26017200	Active TSS	Adipose Nuclei	Adipose
47	chr6:26016800-26017200	Active TSS	Colon Smooth Muscle	Colon
48	chr6:26016800-26017200	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr6:26016800-26017200	Active TSS	Fetal Muscle Trunk	muscle
50	chr6:26016800-26017200	Active TSS	Fetal Stomach	stomach

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