Variant report

Variant	rs9462001
Chromosome Location	chr6:34655563-34655564
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	chr6:34653279..34655876-chr6:34663256..34664778,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196821	Chromatin interaction
ENSG00000272288	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs11961041	0.88[ASN][1000 genomes]
rs11963234	0.85[ASN][1000 genomes]
rs11967912	0.88[ASN][1000 genomes]
rs11968954	0.88[ASN][1000 genomes]
rs11968972	0.88[ASN][1000 genomes]
rs13195490	0.88[ASN][1000 genomes]
rs13196983	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13206245	0.88[ASN][1000 genomes]
rs13209544	0.85[ASN][1000 genomes]
rs13212699	0.80[ASN][1000 genomes]
rs16892384	0.91[ASN][1000 genomes]
rs16892386	0.91[ASN][1000 genomes]
rs205261	0.82[ASN][1000 genomes]
rs205263	0.82[ASN][1000 genomes]
rs205264	0.82[ASN][1000 genomes]
rs205265	0.82[ASN][1000 genomes]
rs205266	0.81[ASN][1000 genomes]
rs205267	0.82[ASN][1000 genomes]
rs34261333	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34374374	0.82[ASN][1000 genomes]
rs34377413	0.91[ASN][1000 genomes]
rs34463942	0.85[ASN][1000 genomes]
rs35081279	0.89[ASN][1000 genomes]
rs35103554	0.82[ASN][1000 genomes]
rs35143960	0.88[ASN][1000 genomes]
rs35186650	0.84[ASN][1000 genomes]
rs35195182	0.86[ASN][1000 genomes]
rs35286877	0.91[ASN][1000 genomes]
rs35369977	0.91[ASN][1000 genomes]
rs35444671	0.85[ASN][1000 genomes]
rs35684630	0.83[ASN][1000 genomes]
rs35744142	0.88[ASN][1000 genomes]
rs35987776	0.91[ASN][1000 genomes]
rs36026951	0.85[ASN][1000 genomes]
rs36032186	0.81[ASN][1000 genomes]
rs4438945	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs451263	0.82[ASN][1000 genomes]
rs451603	0.84[ASN][1000 genomes]
rs6457784	0.81[ASN][1000 genomes]
rs6457792	0.84[ASN][1000 genomes]
rs66672772	0.88[ASN][1000 genomes]
rs66926909	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67622212	0.86[ASN][1000 genomes]
rs67895864	0.89[ASN][1000 genomes]
rs6900426	0.88[ASN][1000 genomes]
rs6908462	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6909393	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6909637	0.91[ASN][1000 genomes]
rs6934741	0.88[ASN][1000 genomes]
rs6937428	0.91[ASN][1000 genomes]
rs6941453	0.85[ASN][1000 genomes]
rs72892238	0.82[ASN][1000 genomes]
rs72892286	0.88[ASN][1000 genomes]
rs72910111	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72910167	0.88[ASN][1000 genomes]
rs7738377	0.84[ASN][1000 genomes]
rs7743724	0.85[ASN][1000 genomes]
rs7748836	0.85[ASN][1000 genomes]
rs7749750	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7758743	0.88[ASN][1000 genomes]
rs7759412	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7759985	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7763989	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7764921	0.88[ASN][1000 genomes]
rs7765969	0.89[ASN][1000 genomes]
rs7775947	0.88[ASN][1000 genomes]
rs7776439	0.88[ASN][1000 genomes]
rs9461992	0.85[ASN][1000 genomes]
rs9461993	0.89[ASN][1000 genomes]
rs9461994	0.91[ASN][1000 genomes]
rs9461997	0.91[ASN][1000 genomes]
rs9462002	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462003	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469813	0.82[ASN][1000 genomes]
rs9469814	0.82[ASN][1000 genomes]
rs9469820	0.85[ASN][1000 genomes]
rs9469822	0.84[ASN][1000 genomes]
rs9469832	0.85[ASN][1000 genomes]
rs9469836	0.91[ASN][1000 genomes]
rs9469837	0.91[ASN][1000 genomes]
rs9469838	0.88[ASN][1000 genomes]
rs9469840	0.91[ASN][1000 genomes]
rs9469842	0.91[ASN][1000 genomes]
rs9469843	0.86[ASN][1000 genomes]
rs9469847	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9469852	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9968782	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2758046	chr6:34382492-34714677	Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759418	chr6:34382492-34714677	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv1033583	chr6:34471572-34828372	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv885793	chr6:34520267-34886436	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv830640	chr6:34542489-34714677	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv885794	chr6:34561585-34673149	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv1032557	chr6:34565802-34802008	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv538196	chr6:34565802-34802008	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	esv2763967	chr6:34566255-34925463	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
13	nsv1020710	chr6:34607214-34890143	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9462001	SNRPC	cis	lung	GTEx
rs9462001	UHRF1BP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34626000-34662000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr6:34626800-34662400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:34633000-34662800	Weak transcription	Aorta	Aorta
4	chr6:34634800-34663200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:34636400-34662200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:34639800-34662800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr6:34639800-34662800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:34640200-34656600	Weak transcription	Spleen	Spleen
9	chr6:34640800-34655800	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:34641400-34662800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:34641800-34656400	Weak transcription	Left Ventricle	heart
12	chr6:34641800-34661200	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:34641800-34663200	Weak transcription	Gastric	stomach
14	chr6:34642200-34656000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:34642200-34663000	Weak transcription	Thymus	Thymus
16	chr6:34643000-34655800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:34643000-34655800	Weak transcription	Lung	lung
18	chr6:34643000-34656400	Weak transcription	Pancreas	Pancrea
19	chr6:34643000-34661200	Weak transcription	Right Atrium	heart
20	chr6:34643000-34662800	Weak transcription	Stomach Mucosa	stomach
21	chr6:34647800-34660800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:34647800-34661000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:34647800-34662000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:34647800-34662200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:34647800-34662400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:34647800-34662600	Weak transcription	Ovary	ovary
27	chr6:34647800-34662800	Weak transcription	Brain Substantia Nigra	brain
28	chr6:34647800-34662800	Weak transcription	HSMMtube	muscle
29	chr6:34648000-34662600	Weak transcription	Right Ventricle	heart
30	chr6:34648000-34662800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr6:34648400-34655800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:34648400-34662000	Weak transcription	Brain Anterior Caudate	brain
33	chr6:34649200-34660200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr6:34649200-34660400	Weak transcription	Primary T cells from cord blood	blood
35	chr6:34649200-34662200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:34649200-34662600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:34649400-34655600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:34649400-34655600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:34649400-34655800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:34649400-34656000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:34649400-34656600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr6:34649400-34656600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr6:34649400-34660200	Weak transcription	NHEK	skin
44	chr6:34649400-34661600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:34649400-34661600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:34649400-34662000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:34649400-34662000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr6:34649400-34662000	Weak transcription	Osteobl	bone
49	chr6:34649400-34662400	Weak transcription	HSMM	muscle
50	chr6:34649600-34661000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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