Variant report

Variant	rs10247585
Chromosome Location	chr7:6229909-6229910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:6097168..6098982-chr7:6228350..6229954,2	MCF-7	breast:
2	chr7:6218147..6221120-chr7:6228782..6230937,2	K562	blood:

Variant related genes	Relation type
ENSG00000086232	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10046499	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs10224504	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10225119	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs10226743	0.85[CHD][hapmap]
rs10228155	1.00[CEU][hapmap]
rs10240510	1.00[JPT][hapmap]
rs10240988	0.85[GIH][hapmap];0.88[MKK][hapmap];0.89[YRI][hapmap]
rs10241174	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[ASN][1000 genomes]
rs10244640	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap]
rs10245186	1.00[JPT][hapmap]
rs10252947	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10253501	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10253733	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10255598	1.00[CEU][hapmap];0.85[CHD][hapmap]
rs10255662	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs10255914	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10261217	1.00[JPT][hapmap]
rs10264140	0.90[ASN][1000 genomes]
rs10267982	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10268916	1.00[CHB][hapmap]
rs10275021	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs10279137	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10280585	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs10951976	0.90[ASN][1000 genomes]
rs10951977	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11768047	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11768749	1.00[JPT][hapmap]
rs12667392	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12669486	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13437890	1.00[JPT][hapmap]
rs17136048	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs17136059	0.82[YRI][hapmap]
rs34123833	0.83[ASN][1000 genomes]
rs58466335	1.00[ASN][1000 genomes]
rs6463540	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6463541	1.00[JPT][hapmap]
rs6463544	1.00[JPT][hapmap]
rs6942707	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap]
rs6944071	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6946205	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6949823	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6955065	1.00[JPT][hapmap]
rs6960965	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap]
rs6962767	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs6969814	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6969863	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7777433	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7780269	1.00[JPT][hapmap]
rs7783018	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7791225	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7800777	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7807841	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs958329	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv5629	chr7:6217866-6263131	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10247585	PMS2CL	cis	multi-tissue	Pritchard

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6202000-6230600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr7:6202400-6238000	Weak transcription	Fetal Kidney	kidney
3	chr7:6209600-6230000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr7:6210000-6230000	Weak transcription	Brain Substantia Nigra	brain
5	chr7:6210800-6230000	Strong transcription	Fetal Stomach	stomach
6	chr7:6211800-6237800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr7:6212200-6237800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:6212600-6231000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:6212800-6238200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr7:6213000-6231200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:6213200-6240600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr7:6215800-6231400	Weak transcription	Hela-S3	cervix
13	chr7:6216800-6237000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr7:6216800-6237800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:6217600-6231600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr7:6217800-6230800	Weak transcription	NH-A	brain
17	chr7:6218600-6230000	Strong transcription	Placenta	Placenta
18	chr7:6218600-6231600	Weak transcription	Brain Hippocampus Middle	brain
19	chr7:6218800-6232000	Weak transcription	Stomach Mucosa	stomach
20	chr7:6219000-6230000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr7:6219000-6233000	Weak transcription	Fetal Heart	heart
22	chr7:6219400-6231600	Strong transcription	Fetal Intestine Small	intestine
23	chr7:6219600-6238000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr7:6219600-6241800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr7:6219600-6243000	Weak transcription	K562	blood
26	chr7:6219800-6241800	Weak transcription	Pancreas	Pancrea
27	chr7:6220200-6232600	Weak transcription	Right Atrium	heart
28	chr7:6221400-6238400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr7:6221800-6230000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr7:6222000-6230000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr7:6222800-6235600	Weak transcription	Psoas Muscle	Psoas
32	chr7:6225400-6230000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr7:6225800-6230000	Strong transcription	Adipose Nuclei	Adipose
34	chr7:6226000-6230000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr7:6226000-6230400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr7:6226600-6230000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr7:6226800-6238200	Weak transcription	Brain Angular Gyrus	brain
38	chr7:6227000-6238600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:6227200-6237600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr7:6227200-6238600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr7:6227200-6239000	Weak transcription	HMEC	breast
42	chr7:6227400-6230200	Weak transcription	Brain Anterior Caudate	brain
43	chr7:6227400-6237600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr7:6227400-6238000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:6227400-6242800	Weak transcription	A549	lung
46	chr7:6228200-6240800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr7:6228400-6230600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr7:6228400-6235600	Weak transcription	Right Ventricle	heart
49	chr7:6228400-6238400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr7:6228600-6247800	Weak transcription	Colon Smooth Muscle	Colon

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