Variant report

Variant	rs6969814
Chromosome Location	chr7:6290751-6290752
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:6289014..6291538-chr7:6312158..6314045,2	MCF-7	breast:
2	chr7:6283219..6284762-chr7:6288057..6290958,2	MCF-7	breast:
3	chr7:6289334..6292556-chr7:6296327..6298930,3	K562	blood:
4	chr7:6290547..6293891-chr7:6295729..6298569,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000008256	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10046499	1.00[JPT][hapmap]
rs10224504	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10225119	1.00[JPT][hapmap]
rs10227013	0.83[ASN][1000 genomes]
rs10240510	1.00[JPT][hapmap]
rs10241174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10241580	1.00[ASN][1000 genomes]
rs10244640	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10245186	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10247585	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10252947	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10253501	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10255662	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10255914	1.00[JPT][hapmap]
rs10261217	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10262194	0.92[YRI][hapmap]
rs10263878	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10267982	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10268916	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10270609	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10274992	0.83[ASN][1000 genomes]
rs10275021	1.00[JPT][hapmap]
rs10279137	1.00[JPT][hapmap]
rs10280585	1.00[JPT][hapmap]
rs11768047	1.00[JPT][hapmap]
rs11768749	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11976961	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12667392	1.00[JPT][hapmap]
rs13237896	0.82[EUR][1000 genomes]
rs13437890	1.00[JPT][hapmap]
rs17136048	1.00[JPT][hapmap]
rs34073302	0.85[EUR][1000 genomes]
rs34312608	0.93[EUR][1000 genomes]
rs34904930	0.85[EUR][1000 genomes]
rs34939060	0.97[EUR][1000 genomes]
rs35257722	0.95[EUR][1000 genomes]
rs35372475	0.85[EUR][1000 genomes]
rs35402521	0.95[EUR][1000 genomes]
rs35868999	0.95[EUR][1000 genomes]
rs35882223	0.95[EUR][1000 genomes]
rs35934233	0.85[EUR][1000 genomes]
rs59180903	0.95[ASN][1000 genomes]
rs59568570	0.83[ASN][1000 genomes]
rs6463535	0.93[EUR][1000 genomes]
rs6463540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6463541	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6463542	0.83[ASN][1000 genomes]
rs6463543	0.83[ASN][1000 genomes]
rs6463544	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6942707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6944071	1.00[JPT][hapmap]
rs6944216	0.95[ASN][1000 genomes]
rs6946205	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6949823	1.00[JPT][hapmap]
rs6955065	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6960965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6961095	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6962767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6969863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6976305	0.83[ASN][1000 genomes]
rs71531366	0.95[EUR][1000 genomes]
rs71531367	0.95[EUR][1000 genomes]
rs71531368	0.95[EUR][1000 genomes]
rs71531370	0.95[EUR][1000 genomes]
rs71531372	0.85[EUR][1000 genomes]
rs71531373	0.82[EUR][1000 genomes]
rs71549618	0.85[EUR][1000 genomes]
rs7777433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7780269	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7780702	0.87[EUR][1000 genomes]
rs7783018	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7783827	0.87[EUR][1000 genomes]
rs7784025	1.00[ASN][1000 genomes]
rs7791225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7800777	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7807841	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7811702	0.83[ASN][1000 genomes]
rs958329	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[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	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
2	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
3	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
5	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
6	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
7	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
8	nsv1021037	chr7:6070792-6426966	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv538713	chr7:6070792-6426966	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription 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	64 gene(s)	inside rSNPs	diseases
10	nsv530989	chr7:6176729-6438197	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv482829	chr7:6231809-6407606	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1032987	chr7:6246313-6373054	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription 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	8 gene(s)	inside rSNPs	diseases
13	nsv538714	chr7:6246313-6373054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6969814	PSCD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6274400-6296000	Weak transcription	Primary B cells from cord blood	blood
2	chr7:6275000-6296000	Weak transcription	Fetal Intestine Small	intestine
3	chr7:6281200-6296000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:6285000-6291600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr7:6286000-6291000	Enhancers	NHDF-Ad	bronchial
6	chr7:6286000-6292600	Enhancers	NHLF	lung
7	chr7:6286400-6291400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:6286400-6295800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:6286800-6291200	Weak transcription	Colon Smooth Muscle	Colon
10	chr7:6286800-6291200	Enhancers	Fetal Muscle Leg	muscle
11	chr7:6286800-6291400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:6286800-6291400	Weak transcription	Hela-S3	cervix
13	chr7:6287000-6291400	Weak transcription	Adipose Nuclei	Adipose
14	chr7:6287000-6291400	Weak transcription	Fetal Kidney	kidney
15	chr7:6287000-6297400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr7:6287400-6291200	Enhancers	Psoas Muscle	Psoas
17	chr7:6287600-6291400	Weak transcription	Fetal Lung	lung
18	chr7:6287600-6291400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr7:6287600-6291600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:6287600-6295000	Weak transcription	Fetal Stomach	stomach
21	chr7:6287800-6292200	Enhancers	HMEC	breast
22	chr7:6288000-6291200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr7:6288000-6293000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr7:6288000-6293000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr7:6288000-6293000	Enhancers	NHEK	skin
26	chr7:6288000-6293400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:6288200-6291400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:6288200-6296000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr7:6288200-6310400	Weak transcription	Brain Angular Gyrus	brain
30	chr7:6288400-6291400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:6288400-6292000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:6288400-6292000	Enhancers	HSMMtube	muscle
33	chr7:6288400-6292800	Weak transcription	Lung	lung
34	chr7:6288400-6295800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:6288400-6296000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr7:6288400-6296400	Weak transcription	Colonic Mucosa	Colon
37	chr7:6288400-6297400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:6288400-6297400	Weak transcription	Ovary	ovary
39	chr7:6288400-6298400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr7:6288400-6300000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr7:6288400-6306600	Weak transcription	Esophagus	oesophagus
42	chr7:6288600-6295800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr7:6288800-6291800	Weak transcription	Brain Hippocampus Middle	brain
44	chr7:6289000-6291400	Weak transcription	HUVEC	blood vessel
45	chr7:6289200-6291000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr7:6289200-6291800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr7:6289200-6292200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr7:6289200-6295000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr7:6289200-6295000	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr7:6289200-6297400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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