Variant report

Variant	rs12492861
Chromosome Location	chr3:121499506-121499507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:121467012..121468872-chr3:121497034..121500161,3	K562	blood:
2	chr3:121498622..121501358-chr3:121516478..121520165,3	K562	blood:
3	chr3:121498095..121500834-chr3:121519561..121521853,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173230	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10470412	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10511407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10934561	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];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915822	1.00[CEU][hapmap]
rs11919421	1.00[CEU][hapmap]
rs12486310	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12486456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488717	0.81[AFR][1000 genomes]
rs12489110	0.81[AFR][1000 genomes]
rs12489686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492214	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];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493927	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs12494523	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12629720	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12636562	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap]
rs13321798	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1881997	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs1881998	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs1919556	0.82[JPT][hapmap]
rs1920307	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1920310	1.00[CHB][hapmap]
rs2222826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293613	1.00[CHB][hapmap]
rs2689278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2700413	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2700414	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28844130	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34241542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35354585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3805129	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41271407	0.81[AFR][1000 genomes]
rs4602434	1.00[CHB][hapmap]
rs4610269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4676761	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs58485759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59064186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59228534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438681	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6798575	0.90[CEU][hapmap]
rs7620562	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs7625960	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs7626052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7643293	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap]
rs7650341	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9834185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9869891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv432483	chr3:121488995-121629634	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv933820	chr3:121489302-121500759	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv934077	chr3:121491540-121507705	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv933987	chr3:121491698-121500759	Strong transcription Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv933526	chr3:121491698-121500853	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv932985	chr3:121491698-121507705	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12492861	HCLS1	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121485600-121503200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:121485800-121501000	Strong transcription	Duodenum Mucosa	Duodenum
3	chr3:121486200-121526600	Weak transcription	Stomach Mucosa	stomach
4	chr3:121486800-121532200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:121487000-121509000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:121487200-121501600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:121487400-121501400	Strong transcription	Primary T cells from cord blood	blood
8	chr3:121487400-121501400	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:121487400-121502000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:121487400-121503000	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:121487400-121512200	Strong transcription	Fetal Thymus	thymus
12	chr3:121487400-121512400	Strong transcription	Dnd41	blood
13	chr3:121487800-121509000	Strong transcription	Fetal Intestine Large	intestine
14	chr3:121487800-121516400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:121487800-121519000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:121488000-121507200	Weak transcription	Brain Substantia Nigra	brain
17	chr3:121488000-121511000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:121488000-121512200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:121488000-121512600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:121488200-121501800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:121488400-121505600	Weak transcription	Fetal Heart	heart
22	chr3:121488400-121509600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:121488600-121501000	Strong transcription	Liver	Liver
24	chr3:121488600-121502000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:121488600-121509000	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:121488600-121510200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr3:121488600-121517800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr3:121489000-121502800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr3:121489000-121509200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr3:121489200-121500600	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:121489200-121501400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr3:121489600-121507000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr3:121489800-121506200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:121489800-121506400	Weak transcription	Gastric	stomach
35	chr3:121489800-121508000	Weak transcription	Esophagus	oesophagus
36	chr3:121489800-121508800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:121489800-121510600	Weak transcription	Spleen	Spleen
38	chr3:121489800-121514800	Weak transcription	Small Intestine	intestine
39	chr3:121489800-121529800	Weak transcription	Aorta	Aorta
40	chr3:121490000-121529800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:121490000-121529800	Weak transcription	Pancreas	Pancrea
42	chr3:121490400-121501000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr3:121491600-121499600	Weak transcription	NHEK	skin
44	chr3:121491600-121506600	Weak transcription	NHDF-Ad	bronchial
45	chr3:121491600-121507000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:121491600-121552600	Weak transcription	NHLF	lung
47	chr3:121491800-121499600	Weak transcription	Thymus	Thymus
48	chr3:121492800-121501600	Strong transcription	GM12878-XiMat	blood
49	chr3:121493200-121501400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:121493200-121502400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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