Variant report

Variant	rs540124
Chromosome Location	chr9:97328175-97328176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97322497..97324885-chr9:97327603..97329721,3	K562	blood:
2	chr9:97328083..97332343-chr9:97333788..97336577,4	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10115929	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10119419	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1042144	0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs10733753	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10761331	0.83[ASN][1000 genomes]
rs10761332	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10761333	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10821364	0.84[ASN][1000 genomes]
rs10821365	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10821367	0.87[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10821369	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10993241	0.81[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10993242	0.87[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10993275	0.81[TSI][hapmap]
rs11790263	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16937175	1.00[ASW][hapmap]
rs1754435	0.81[JPT][hapmap];0.84[TSI][hapmap]
rs1754439	1.00[ASW][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2280300	0.87[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2460138	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2479602	1.00[MKK][hapmap]
rs2679599	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2679600	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2679602	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2772013	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2772022	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2790390	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2945802	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2987882	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2993958	0.81[JPT][hapmap];0.84[TSI][hapmap]
rs2993961	0.81[JPT][hapmap];0.84[TSI][hapmap]
rs3864788	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4743961	0.84[TSI][hapmap]
rs4744346	1.00[MKK][hapmap]
rs4744353	0.87[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4744362	0.82[ASW][hapmap];0.84[TSI][hapmap]
rs479197	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs514222	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs515339	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs518768	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs539320	0.85[EUR][1000 genomes]
rs543731	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs548348	0.81[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs576745	0.95[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs583365	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs590090	0.91[AFR][1000 genomes]
rs598386	0.81[JPT][hapmap]
rs632506	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs652867	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs688165	1.00[MKK][hapmap]
rs688843	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs693399	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7024700	0.95[CEU][hapmap]
rs7048277	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs781650	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7867912	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs802918	0.84[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs802919	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8192689	0.84[TSI][hapmap]
rs874248	0.81[JPT][hapmap];0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs965474	0.87[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv893595	chr9:97268182-97330693	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs540124	HIATL1	cis	parietal	SCAN
rs540124	PHF2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97317200-97354000	Weak transcription	Gastric	stomach
2	chr9:97317600-97328600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr9:97318200-97332000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:97318800-97331600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:97319200-97331800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:97320800-97330600	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr9:97322800-97329200	Weak transcription	Liver	Liver
8	chr9:97322800-97331400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:97322800-97331800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:97323000-97331400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:97324200-97330000	Weak transcription	Psoas Muscle	Psoas
12	chr9:97325800-97329200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr9:97325800-97329200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr9:97325800-97331600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr9:97325800-97331600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:97325800-97331800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr9:97325800-97339200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:97326000-97331400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:97326800-97339200	Weak transcription	Fetal Stomach	stomach

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