Variant report

Variant	rs227849
Chromosome Location	chr6:44698708-44698709
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:44629072..44631596-chr6:44697653..44700254,3	MCF-7	breast:
2	chr6:44698581..44700175-chr6:45387689..45389869,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271857	Chromatin interaction
ENSG00000124813	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10484627	0.84[CHB][hapmap]
rs10948183	0.95[CHB][hapmap]
rs12190136	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12192367	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12215252	0.93[EUR][1000 genomes]
rs12525009	0.84[CHB][hapmap]
rs12526711	0.82[CHB][hapmap]
rs1293457	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1293467	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1338907	0.93[EUR][1000 genomes]
rs1342370	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1342640	0.91[EUR][1000 genomes]
rs1418433	0.90[EUR][1000 genomes]
rs1418434	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1557143	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17422760	0.84[CHB][hapmap];0.82[MEX][hapmap]
rs1832897	0.91[EUR][1000 genomes]
rs1891411	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1891412	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1935551	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2038555	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2038556	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2038557	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2040032	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs227831	0.81[EUR][1000 genomes]
rs227837	0.86[EUR][1000 genomes]
rs227838	0.89[EUR][1000 genomes]
rs227841	0.89[EUR][1000 genomes]
rs227844	0.82[ASN][1000 genomes]
rs227845	0.85[ASN][1000 genomes]
rs227847	0.92[EUR][1000 genomes]
rs227848	0.94[EUR][1000 genomes]
rs227850	0.93[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs227851	0.92[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs227852	0.90[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs227853	0.90[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs227855	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs34577161	0.84[ASN][1000 genomes]
rs3778507	0.95[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap]
rs3799967	0.85[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.82[ASN][1000 genomes]
rs3799968	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes]
rs3799971	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs3799973	0.94[CHB][hapmap]
rs3799976	0.89[CHB][hapmap]
rs3799977	0.89[CHB][hapmap]
rs3799979	0.89[CHB][hapmap]
rs3799981	0.89[CHB][hapmap]
rs3799984	0.89[CHB][hapmap]
rs4711797	0.81[ASN][1000 genomes]
rs4711798	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4711799	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4714812	0.90[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4714819	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4714820	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4714821	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4714822	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4714828	0.89[CHB][hapmap]
rs538801	0.89[CHB][hapmap]
rs59881382	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs608941	0.89[CHB][hapmap]
rs6458412	0.93[EUR][1000 genomes]
rs6458415	0.85[CEU][hapmap];0.95[CHB][hapmap];0.81[YRI][hapmap]
rs6904015	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6910294	0.88[CEU][hapmap];0.95[CHB][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6910749	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs71564699	0.83[AMR][1000 genomes]
rs764396	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs764397	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7754378	0.95[CHB][hapmap];0.82[MEX][hapmap]
rs7754698	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs911524	0.90[EUR][1000 genomes]
rs929614	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9349303	0.85[CEU][hapmap]
rs9357459	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9367211	0.85[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.81[YRI][hapmap]
rs9369512	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9369513	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9369514	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.82[ASN][1000 genomes]
rs9369516	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap]
rs9395049	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap]
rs9395051	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap]
rs9472331	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs9472336	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9472339	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9472360	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817071	chr6:44670110-44698829	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs227849	SUPT3H	cis	cerebellum	SCAN
rs227849	SUPT3H	cis	multi-tissue	Pritchard
rs227849	C6orf226	cis	cerebellum	SCAN
rs227849	SUPT3H	cis	lymphoblastoid	seeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44695800-44701000	Weak transcription	Pancreas	Pancrea
2	chr6:44695800-44703600	Weak transcription	Esophagus	oesophagus
3	chr6:44696000-44706000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:44697600-44699800	Enhancers	Fetal Kidney	kidney
5	chr6:44697800-44704200	Enhancers	Colon Smooth Muscle	Colon
6	chr6:44698000-44698800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:44698000-44700000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr6:44698000-44700400	Enhancers	HSMMtube	muscle
9	chr6:44698200-44699200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:44698200-44699200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:44698200-44699200	Bivalent Enhancer	Fetal Muscle Leg	muscle
12	chr6:44698200-44699200	Enhancers	NH-A	brain
13	chr6:44698200-44699600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:44698200-44699600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr6:44698200-44699600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:44698200-44699800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:44698200-44699800	Enhancers	HSMM	muscle
18	chr6:44698200-44703800	Enhancers	Placenta	Placenta
19	chr6:44698400-44699200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:44698400-44699400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:44698400-44699600	Enhancers	Fetal Intestine Small	intestine
22	chr6:44698400-44699600	Enhancers	Fetal Stomach	stomach
23	chr6:44698400-44699800	Enhancers	Fetal Intestine Large	intestine
24	chr6:44698400-44699800	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr6:44698400-44699800	Enhancers	Rectal Smooth Muscle	rectum
26	chr6:44698400-44699800	Enhancers	NHLF	lung
27	chr6:44698400-44699800	Enhancers	Osteobl	bone
28	chr6:44698400-44700200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr6:44698400-44700600	Enhancers	Fetal Muscle Trunk	muscle
30	chr6:44698600-44698800	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr6:44698600-44699000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:44698600-44699600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:44698600-44701200	Weak transcription	Fetal Lung	lung
34	chr6:44698600-44701200	Weak transcription	GM12878-XiMat	blood

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