Variant report

Variant	rs10947627
Chromosome Location	chr6:36708989-36708990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36708140..36710606-chr6:36718569..36720077,2	MCF-7	breast:
2	chr6:36588827..36591407-chr6:36708568..36710825,2	MCF-7	breast:
3	chr6:36708174..36711394-chr6:36720287..36721932,3	MCF-7	breast:
4	chr6:36706791..36710785-chr6:36712838..36716064,4	MCF-7	breast:
5	chr6:36646178..36648267-chr6:36708912..36712169,4	MCF-7	breast:
6	chr6:36708918..36710565-chr6:36712727..36715586,2	K562	blood:

Variant related genes	Relation type
ENSG00000263894	Chromatin interaction
ENSG00000124762	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1010791	0.81[ASW][hapmap]
rs1065258	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1065259	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1065260	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1065261	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12194367	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12196180	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13193217	0.86[CHB][hapmap]
rs1864750	0.80[ASW][hapmap];0.81[YRI][hapmap]
rs236473	0.86[CHB][hapmap]
rs2395662	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6904294	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743870	0.95[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs7741255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763347	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9470385	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
3	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv885809	chr6:36687518-36719079	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv885810	chr6:36695223-36714491	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv885811	chr6:36695223-36719079	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv524053	chr6:36695223-36747406	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
10	nsv520755	chr6:36702284-36713720	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv885813	chr6:36702843-36713720	Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	nsv525168	chr6:36704787-36713720	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv885814	chr6:36704807-36722842	Enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
14	nsv602951	chr6:36706157-36719079	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10947627	PIM1	cis	cerebellum	SCAN
rs10947627	NUDT3	cis	cerebellum	SCAN
rs10947627	PNPLA1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36703400-36710200	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr6:36703400-36718000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:36703600-36709000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:36703800-36711400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:36703800-36712800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:36703800-36718000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:36704000-36709200	Weak transcription	Esophagus	oesophagus
8	chr6:36704000-36709400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:36704000-36709800	Weak transcription	Fetal Stomach	stomach
10	chr6:36704000-36711600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr6:36704000-36711800	Weak transcription	Brain Anterior Caudate	brain
12	chr6:36704000-36712600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:36704000-36718000	Weak transcription	Right Atrium	heart
14	chr6:36704000-36720400	Weak transcription	Right Ventricle	heart
15	chr6:36704200-36709200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:36704200-36709400	Weak transcription	Stomach Mucosa	stomach
17	chr6:36704200-36710200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:36704200-36711800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr6:36705600-36710000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:36706800-36709400	Enhancers	HUVEC	blood vessel
21	chr6:36707000-36709200	Enhancers	Adipose Nuclei	Adipose
22	chr6:36707200-36709600	Enhancers	Primary B cells from cord blood	blood
23	chr6:36707400-36709200	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr6:36707400-36709200	Enhancers	Spleen	Spleen
25	chr6:36707600-36710800	Weak transcription	Gastric	stomach
26	chr6:36707600-36712600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr6:36707800-36711200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:36707800-36711200	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr6:36708000-36711200	Enhancers	Colonic Mucosa	Colon
30	chr6:36708200-36710000	Enhancers	Fetal Muscle Leg	muscle
31	chr6:36708200-36711000	Weak transcription	NHLF	lung
32	chr6:36708400-36720800	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr6:36708800-36709400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr6:36708800-36710600	Enhancers	Fetal Intestine Small	intestine

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