Variant report

Variant	rs12212242
Chromosome Location	chr6:31768971-31768972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:31767775..31769625-chr6:31827147..31829502,2	K562	blood:
2	chr6:31767735..31770421-chr6:31830479..31834211,3	K562	blood:
3	chr6:31760037..31761914-chr6:31767619..31769119,2	MCF-7	breast:
4	chr6:31767528..31770908-chr6:31772125..31775627,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204386	Chromatin interaction
ENSG00000204394	Chromatin interaction
ENSG00000204392	Chromatin interaction
ENSG00000204385	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11968400	0.94[ASN][1000 genomes]
rs12193504	1.00[ASN][1000 genomes]
rs12206352	0.86[EUR][1000 genomes]
rs12210887	0.94[ASN][1000 genomes]
rs12213612	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13191375	1.00[ASN][1000 genomes]
rs3869144	0.97[ASN][1000 genomes]
rs693906	0.97[ASN][1000 genomes]
rs73400280	0.97[ASN][1000 genomes]
rs7765136	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
10	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
11	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
12	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases
13	nsv884426	chr6:31728102-31800868	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
14	nsv884427	chr6:31728102-31802465	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
15	nsv884428	chr6:31728102-31870326	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
16	nsv884429	chr6:31730356-31837066	Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
17	nsv884430	chr6:31731881-31800631	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
18	nsv884432	chr6:31734117-31777687	Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
19	nsv884433	chr6:31737701-31777687	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
20	nsv884437	chr6:31739881-31777687	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
21	nsv884440	chr6:31743882-31775984	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription 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	57 gene(s)	inside rSNPs	diseases
22	nsv884443	chr6:31745518-31777687	Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription 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 miRNA target site	50 gene(s)	inside rSNPs	diseases
23	nsv884445	chr6:31756907-31769250	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	37 gene(s)	inside rSNPs	diseases
24	nsv884446	chr6:31760309-31768971	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	37 gene(s)	inside rSNPs	diseases
25	nsv884447	chr6:31760654-31770770	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12212242	HSPA1L	cis	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31763600-31773600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:31763800-31773600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:31763800-31773800	Weak transcription	Gastric	stomach
4	chr6:31764000-31769000	Weak transcription	Spleen	Spleen
5	chr6:31764000-31773400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:31764000-31773600	Weak transcription	Fetal Kidney	kidney
7	chr6:31764000-31773600	Weak transcription	HSMMtube	muscle
8	chr6:31764000-31773600	Weak transcription	NHDF-Ad	bronchial
9	chr6:31764000-31773600	Weak transcription	NHLF	lung
10	chr6:31764000-31773800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:31764000-31773800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:31764000-31773800	Weak transcription	Esophagus	oesophagus
13	chr6:31764000-31774000	Weak transcription	Aorta	Aorta
14	chr6:31764000-31774000	Weak transcription	Ovary	ovary
15	chr6:31764200-31769000	Weak transcription	Small Intestine	intestine
16	chr6:31764200-31769200	Weak transcription	Lung	lung
17	chr6:31764200-31769600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:31764200-31770200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:31764200-31771400	Weak transcription	Right Atrium	heart
20	chr6:31764200-31773000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:31764200-31773400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:31764200-31773400	Weak transcription	Osteobl	bone
23	chr6:31764200-31773600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:31764200-31773600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:31764200-31773600	Weak transcription	Liver	Liver
26	chr6:31764200-31773600	Weak transcription	Brain Angular Gyrus	brain
27	chr6:31764200-31773600	Weak transcription	Brain Anterior Caudate	brain
28	chr6:31764200-31773600	Weak transcription	Brain Substantia Nigra	brain
29	chr6:31764200-31773600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr6:31764200-31773600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:31764200-31773600	Weak transcription	Psoas Muscle	Psoas
32	chr6:31764200-31773600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr6:31764200-31773600	Weak transcription	A549	lung
34	chr6:31764200-31773600	Weak transcription	HSMM	muscle
35	chr6:31764200-31773800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:31764200-31773800	Weak transcription	Right Ventricle	heart
37	chr6:31764200-31773800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr6:31764200-31774000	Weak transcription	Left Ventricle	heart
39	chr6:31764400-31769200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:31764400-31773400	Weak transcription	Hela-S3	cervix
41	chr6:31764400-31773600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr6:31764400-31773600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr6:31764400-31773600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:31764400-31773600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:31764400-31773600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:31764400-31773600	Weak transcription	Colonic Mucosa	Colon
47	chr6:31764400-31773600	Weak transcription	Colon Smooth Muscle	Colon
48	chr6:31764400-31773600	Weak transcription	Pancreas	Pancrea
49	chr6:31764400-31773600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:31764400-31773600	Weak transcription	Stomach Mucosa	stomach

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