Variant report

Variant	rs6905862
Chromosome Location	chr6:31127602-31127603
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr6:31127039-31127623	GM12878	blood:	n/a	n/a
2	WRNIP1	chr6:31127521-31127917	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:31125636-31127732	GM12892	blood:	n/a	n/a
4	CTCF	chr6:31127600-31127750	GM12872	blood:	n/a	n/a
5	CTCF	chr6:31127520-31127670	HFF-Myc	foreskin:	n/a	n/a
6	POLR2A	chr6:31127056-31127626	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:31127023-31127638	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:31126559-31127652	A549	lung:	n/a	n/a
9	MTA3	chr6:31126058-31128087	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:31125655-31128143	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr6:31127097-31127842	H1-hESC	embryonic stem cell:	n/a	n/a
12	ELF1	chr6:31127035-31127633	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:31127083-31127683	A549	lung:	n/a	n/a
14	POLR2A	chr6:31127012-31127640	A549	lung:	n/a	n/a
15	POLR2A	chr6:31126717-31127953	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr6:31126119-31128136	GM12892	blood:	n/a	n/a
17	POLR2A	chr6:31127601-31127675	HepG2	liver:	n/a	n/a
18	POLR2A	chr6:31127107-31127710	H1-hESC	embryonic stem cell:	n/a	n/a
19	KAP1	chr6:31126989-31127671	HEK293	kidney:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31125954..31128399-chr6:31147370..31149956,2	MCF-7	breast:
2	chr6:31124835..31127745-chr6:31135310..31138711,4	MCF-7	breast:
3	chr6:31126958..31132315-chr6:31135299..31140140,6	K562	blood:
4	chr6:31103022..31109591-chr6:31125707..31129394,9	MCF-7	breast:

No data

Variant related genes	Relation type
TCF19	TF binding region
CCHCR1	TF binding region
ENSG00000204540	Chromatin interaction
ENSG00000204531	Chromatin interaction
ENSG00000204538	Chromatin interaction
ENSG00000238211	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs130066	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13409	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419881	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2077010	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3130453	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs885950	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs885951	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv525933	chr6:31081205-31142245	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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	25 gene(s)	inside rSNPs	diseases
12	nsv884137	chr6:31082361-31129310	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS 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	22 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	nsv524061	chr6:31107087-31133943	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	nsv884138	chr6:31114573-31129707	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6905862	SNRPC	cis	parietal	SCAN
rs6905862	CCHCR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31125000-31127800	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:31125200-31127800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:31125400-31127800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:31125400-31128000	Active TSS	GM12878-XiMat	blood
5	chr6:31125600-31127800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr6:31126400-31127800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:31126400-31127800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr6:31126400-31128000	Flanking Active TSS	Fetal Muscle Leg	muscle
9	chr6:31126600-31127800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:31126600-31127800	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr6:31126600-31127800	Flanking Active TSS	Fetal Muscle Trunk	muscle
12	chr6:31126600-31128000	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr6:31126600-31128000	Enhancers	Spleen	Spleen
14	chr6:31126600-31128200	Flanking Active TSS	HUVEC	blood vessel
15	chr6:31126800-31127800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr6:31126800-31127800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr6:31126800-31127800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:31126800-31127800	Enhancers	Lung	lung
19	chr6:31126800-31127800	Flanking Active TSS	Osteobl	bone
20	chr6:31126800-31128000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:31126800-31128000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:31126800-31128000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:31126800-31128000	Flanking Active TSS	NHEK	skin
24	chr6:31127000-31127800	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr6:31127000-31128000	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr6:31127000-31128000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:31127000-31128000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:31127000-31128200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:31127000-31128200	Transcr. at gene 5' and 3'	Dnd41	blood
30	chr6:31127000-31128200	Flanking Active TSS	HMEC	breast
31	chr6:31127200-31127800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
32	chr6:31127200-31127800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:31127200-31127800	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr6:31127200-31127800	Enhancers	Primary T cells from cord blood	blood
35	chr6:31127200-31127800	Enhancers	Primary T cells fromperipheralblood	blood
36	chr6:31127200-31127800	Enhancers	Primary hematopoietic stem cells	blood
37	chr6:31127200-31127800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr6:31127200-31127800	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr6:31127200-31127800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:31127200-31127800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:31127200-31127800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr6:31127200-31127800	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr6:31127200-31127800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:31127200-31127800	Enhancers	Adipose Nuclei	Adipose
45	chr6:31127200-31127800	Enhancers	Colon Smooth Muscle	Colon
46	chr6:31127200-31127800	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr6:31127200-31127800	Active TSS	Rectal Smooth Muscle	rectum
48	chr6:31127200-31127800	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr6:31127200-31127800	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr6:31127200-31127800	Flanking Active TSS	HepG2	liver

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