Variant report

Variant	rs915660
Chromosome Location	chr6:31143835-31143836
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:31136072..31138764-chr6:31142991..31146892,3	MCF-7	breast:
2	chr6:31124577..31126199-chr6:31142566..31144276,2	MCF-7	breast:
3	chr6:31136662..31139388-chr6:31141163..31144214,3	K562	blood:
4	chr6:31135382..31137193-chr6:31141823..31144114,2	MCF-7	breast:
5	chr6:31141777..31144168-chr6:31146609..31148778,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCHCR1-1	chr6:31142015-31144598	XLOC_005677

Variant related genes	Relation type
ENSG00000204531	Chromatin interaction
ENSG00000204536	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1052989	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11381232	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11507945	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11961945	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11961983	0.90[AFR][1000 genomes]
rs11967629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1265160	0.94[AFR][1000 genomes]
rs1265163	0.94[AFR][1000 genomes]
rs28360055	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28360056	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28360057	0.93[AFR][1000 genomes]
rs28360058	0.93[AFR][1000 genomes]
rs28360059	0.93[AFR][1000 genomes]
rs28360060	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28360061	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28360062	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28360063	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28360064	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs28360065	0.82[ASN][1000 genomes]
rs28360067	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28397268	0.88[ASN][1000 genomes]
rs28397269	0.83[AFR][1000 genomes]
rs28397270	0.90[ASN][1000 genomes]
rs28397271	0.90[ASN][1000 genomes]
rs28397273	0.87[ASN][1000 genomes]
rs28397274	0.86[ASN][1000 genomes]
rs28397276	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28397277	0.90[AFR][1000 genomes]
rs28397282	0.91[ASN][1000 genomes]
rs28397284	0.90[AFR][1000 genomes]
rs28397285	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs28397286	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28749548	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs28749549	0.93[AFR][1000 genomes]
rs28749550	0.93[AFR][1000 genomes]
rs28749551	0.90[AFR][1000 genomes]
rs34467061	0.91[ASN][1000 genomes]
rs4122189	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4713441	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713442	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6899874	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6899875	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6901685	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6921663	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6922077	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6922553	0.91[ASN][1000 genomes]
rs6922756	0.90[ASN][1000 genomes]
rs6922842	0.87[ASN][1000 genomes]
rs6922994	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6927253	0.90[ASN][1000 genomes]
rs6936474	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6936597	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6941912	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7741829	0.84[ASN][1000 genomes]
rs7755702	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7772290	0.85[ASN][1000 genomes]
rs887464	0.84[ASN][1000 genomes]
rs9263852	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9263869	0.80[ASN][1000 genomes]
rs9295957	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295958	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9357109	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357113	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9357115	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9366769	0.90[ASN][1000 genomes]
rs9368661	0.81[ASN][1000 genomes]
rs9368662	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9368663	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9378115	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380220	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380221	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380222	0.91[ASN][1000 genomes]
rs9380223	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9391712	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9391815	0.82[ASN][1000 genomes]
rs9391818	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9394042	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9404983	0.91[ASN][1000 genomes]
rs9405052	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9468882	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' 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	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv1019637	chr6:31104401-31354706	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
12	nsv1029569	chr6:31104401-31412740	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
13	nsv538174	chr6:31104401-31412740	Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
14	nsv1034391	chr6:31131121-31279595	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
15	nsv1025909	chr6:31131121-31354706	Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
16	nsv538175	chr6:31131121-31354706	Active TSS Bivalent Enhancer Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
17	nsv1015890	chr6:31131121-31449207	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
18	nsv538176	chr6:31131121-31449207	Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
19	esv32635	chr6:31141504-31250618	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs915660	CCHCR1	Cis_1M	lymphoblastoid	RTeQTL
rs915660	TCF19	Cis_1M	lymphoblastoid	RTeQTL
rs915660	HLA-B	Cis_1M	lymphoblastoid	RTeQTL
rs915660	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs915660	TCF19	cis	multi-tissue	Pritchard
rs915660	CCHCR1	cis	multi-tissue	Pritchard
rs915660	HLA-F	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31127200-31146800	Weak transcription	Small Intestine	intestine
2	chr6:31127600-31147800	Weak transcription	Primary B cells from cord blood	blood
3	chr6:31127600-31148000	Weak transcription	Right Atrium	heart
4	chr6:31127800-31146200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:31127800-31147800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:31127800-31147800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:31127800-31153200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:31130200-31146200	Weak transcription	Lung	lung
9	chr6:31130400-31147800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:31130600-31146800	Weak transcription	Colonic Mucosa	Colon
11	chr6:31131000-31147800	Weak transcription	Adipose Nuclei	Adipose
12	chr6:31131000-31148000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:31131000-31148000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr6:31132000-31148000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:31133000-31148000	Weak transcription	Thymus	Thymus
16	chr6:31133000-31148200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:31134200-31145800	Weak transcription	GM12878-XiMat	blood
18	chr6:31138000-31146600	Weak transcription	Spleen	Spleen
19	chr6:31138000-31146800	Weak transcription	Hela-S3	cervix
20	chr6:31138000-31157400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr6:31139400-31148000	Weak transcription	Fetal Intestine Small	intestine
22	chr6:31140000-31145200	Weak transcription	Stomach Mucosa	stomach
23	chr6:31141200-31144000	Enhancers	H1 Cell Line	embryonic stem cell
24	chr6:31141400-31144200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr6:31141400-31146800	Weak transcription	Left Ventricle	heart
26	chr6:31141400-31148200	Weak transcription	Brain Germinal Matrix	brain
27	chr6:31141400-31148400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:31141600-31148000	Weak transcription	A549	lung
29	chr6:31141800-31144200	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr6:31141800-31152400	Weak transcription	HMEC	breast
31	chr6:31141800-31164800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:31142000-31144000	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr6:31142200-31144200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr6:31142200-31147600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr6:31142800-31144200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:31142800-31144200	Genic enhancers	Pancreas	Pancrea
37	chr6:31142800-31144400	Enhancers	HSMM	muscle
38	chr6:31142800-31144600	Enhancers	Fetal Muscle Leg	muscle
39	chr6:31142800-31148800	Strong transcription	HepG2	liver
40	chr6:31143000-31144000	Enhancers	Fetal Muscle Trunk	muscle
41	chr6:31143000-31146800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr6:31143200-31144000	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr6:31143200-31144000	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr6:31143200-31144200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:31143200-31144200	Enhancers	Fetal Heart	heart
46	chr6:31143200-31144400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:31143200-31144400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:31143200-31144400	Enhancers	K562	blood
49	chr6:31143200-31144600	Enhancers	NHLF	lung
50	chr6:31143200-31147800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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