Variant report

Variant	rs7750470
Chromosome Location	chr6:45473256-45473257
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45387751..45393702-chr6:45470128..45480232,15	MCF-7	breast:
2	chr6:45472331..45474237-chr6:45572643..45575608,3	MCF-7	breast:
3	chr6:45465666..45468253-chr6:45472384..45474862,2	MCF-7	breast:
4	chr6:45468999..45471177-chr6:45472173..45475442,3	K562	blood:
5	chr6:45473234..45474923-chr6:45476629..45478721,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271857	Chromatin interaction
ENSG00000124813	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12665523	0.93[JPT][hapmap]
rs16873429	0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs16873437	0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs1934328	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs2396441	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs62400362	0.97[EUR][1000 genomes]
rs62400365	0.95[EUR][1000 genomes]
rs6914610	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7750266	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs7754227	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7773875	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7750470	SUPT3H	cis	parietal	SCAN
rs7750470	CENPQ	cis	cerebellum	SCAN
rs7750470	CYP39A1	cis	cerebellum	SCAN
rs7750470	GUCA1B	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45461200-45480000	Weak transcription	NHDF-Ad	bronchial
2	chr6:45464800-45479800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr6:45465000-45479400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:45465000-45480000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:45465000-45521600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr6:45465800-45480000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:45466000-45480200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr6:45466400-45483400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:45466800-45488200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:45466800-45497200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:45467200-45475400	Weak transcription	Small Intestine	intestine
12	chr6:45467200-45480000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr6:45467200-45487800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:45467400-45480000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:45467600-45480000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr6:45469800-45473400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:45469800-45473800	Enhancers	Hela-S3	cervix
18	chr6:45469800-45474000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:45470200-45475000	Genic enhancers	HSMM	muscle
20	chr6:45471000-45473400	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr6:45471000-45479000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr6:45471200-45473600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr6:45471200-45474000	Enhancers	Fetal Thymus	thymus
24	chr6:45471600-45473600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:45471600-45474600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:45471800-45473400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:45471800-45473600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:45471800-45473600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:45471800-45473600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:45471800-45473800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:45471800-45474000	Enhancers	H1 Cell Line	embryonic stem cell
32	chr6:45471800-45474200	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr6:45471800-45474800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr6:45472000-45473400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:45472000-45473600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr6:45472000-45473600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:45472000-45473800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:45472000-45473800	Enhancers	NHLF	lung
39	chr6:45472000-45474000	Enhancers	Primary T cells from cord blood	blood
40	chr6:45472000-45474000	Enhancers	Dnd41	blood
41	chr6:45472000-45474200	Enhancers	H9 Cell Line	embryonic stem cell
42	chr6:45472000-45477200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr6:45472200-45473400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr6:45472200-45473600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr6:45472200-45473600	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr6:45472200-45473800	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr6:45472200-45473800	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr6:45472200-45482400	Weak transcription	Spleen	Spleen
49	chr6:45472400-45473400	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr6:45472400-45473400	Enhancers	Fetal Stomach	stomach

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