Variant report

Variant	rs6899874
Chromosome Location	chr6:31162328-31162329
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31162217-31162407	K562	blood:	n/a	n/a
2	BCL3	chr6:31162149-31162491	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:31088553..31090174-chr6:31161493..31163049,2	K562	blood:

Variant related genes	Relation type
HCG27	TF binding region

Extended variants
information (count: 106 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1052989	0.92[ASN][1000 genomes]
rs1135811	0.89[EUR][1000 genomes]
rs11381232	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11507945	0.92[ASN][1000 genomes]
rs11961983	0.88[AFR][1000 genomes]
rs11967629	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17197540	0.89[EUR][1000 genomes]
rs28360055	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28360056	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28360057	0.85[AFR][1000 genomes]
rs28360058	0.85[AFR][1000 genomes]
rs28360059	0.85[AFR][1000 genomes]
rs28360060	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28360061	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28360062	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28360063	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs28360064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28360065	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28360066	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28360067	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs28397268	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28397269	0.81[AFR][1000 genomes]
rs28397270	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28397271	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28397273	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28397274	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28397276	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28397277	0.88[AFR][1000 genomes]
rs28397282	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28397284	0.88[AFR][1000 genomes]
rs28397285	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28397286	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28749548	0.82[AFR][1000 genomes]
rs28749549	0.85[AFR][1000 genomes]
rs28749550	0.85[AFR][1000 genomes]
rs28749551	0.88[AFR][1000 genomes]
rs34467061	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4122189	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713441	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4713442	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6899875	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6901685	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6907451	0.89[EUR][1000 genomes]
rs6913470	0.85[EUR][1000 genomes]
rs6913863	0.88[EUR][1000 genomes]
rs6921663	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6922077	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6922553	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6922756	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6922842	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6922994	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6927253	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6930438	0.89[EUR][1000 genomes]
rs6936474	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6936597	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6941912	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7453202	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7741829	0.90[ASN][1000 genomes]
rs7755702	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7772290	0.91[ASN][1000 genomes]
rs887464	0.90[ASN][1000 genomes]
rs915660	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9263869	0.87[ASN][1000 genomes]
rs9263875	0.86[ASN][1000 genomes]
rs9295957	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9295958	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9295960	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9357109	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9357113	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9357115	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9366769	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9368662	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9368663	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9378115	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9378227	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9380220	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9380221	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9380222	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380223	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9391712	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9391815	0.85[ASN][1000 genomes]
rs9391818	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9391819	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9394042	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9404983	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9405052	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9468882	0.90[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6899874	HCG27	cis	multi-tissue	Pritchard
rs6899874	DDR1	cis	lymphoblastoid	seeQTL
rs6899874	HLA-B	cis	lymphoblastoid	seeQTL
rs6899874	TCF19	cis	lymphoblastoid	seeQTL
rs6899874	CCHCR1	cis	multi-tissue	Pritchard
rs6899874	HLA-C	cis	multi-tissue	Pritchard
rs6899874	CCHCR1	cis	lymphoblastoid	seeQTL
rs6899874	NKAPL	cis	parietal	SCAN
rs6899874	TCF19	cis	multi-tissue	Pritchard

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31141800-31164800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:31148800-31164000	Weak transcription	Primary B cells from cord blood	blood
3	chr6:31153400-31162400	Weak transcription	Spleen	Spleen
4	chr6:31154200-31164200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:31154200-31164200	Weak transcription	Psoas Muscle	Psoas
6	chr6:31154200-31164400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:31154200-31164600	Weak transcription	Left Ventricle	heart
8	chr6:31154200-31164600	Weak transcription	Right Atrium	heart
9	chr6:31154400-31164000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr6:31154400-31164200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr6:31154400-31164200	Weak transcription	Adipose Nuclei	Adipose
12	chr6:31154400-31164200	Weak transcription	Liver	Liver
13	chr6:31154400-31164600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:31154400-31164800	Weak transcription	Gastric	stomach
15	chr6:31155200-31162600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:31155200-31164200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr6:31155400-31164400	Weak transcription	Pancreas	Pancrea
18	chr6:31155400-31164800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:31155600-31162400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr6:31155600-31164200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr6:31157400-31162600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:31157400-31164600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:31157400-31164800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:31158800-31164400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr6:31159000-31164200	Weak transcription	GM12878-XiMat	blood
26	chr6:31159400-31164200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr6:31160600-31164600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:31160800-31164800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:31161000-31162400	Strong transcription	Primary T cells from cord blood	blood
30	chr6:31161000-31162400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:31161200-31162400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr6:31161200-31162600	Weak transcription	Dnd41	blood
33	chr6:31161200-31163400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:31161200-31164600	Weak transcription	Brain Anterior Caudate	brain
35	chr6:31161800-31162400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:31161800-31164600	Weak transcription	Thymus	Thymus
37	chr6:31162000-31162400	Enhancers	Primary hematopoietic stem cells	blood
38	chr6:31162000-31162800	Genic enhancers	Primary B cells from peripheral blood	blood
39	chr6:31162000-31162800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:31162000-31162800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:31162000-31162800	Enhancers	Colon Smooth Muscle	Colon
42	chr6:31162000-31162800	Enhancers	Fetal Lung	lung
43	chr6:31162000-31162800	Enhancers	Lung	lung
44	chr6:31162000-31163000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:31162000-31164200	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr6:31162200-31162400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr6:31162200-31162600	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr6:31162200-31162600	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr6:31162200-31162600	Weak transcription	Brain Angular Gyrus	brain
50	chr6:31162200-31162800	Enhancers	Primary T helper naive cells from peripheral blood	blood

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