Variant report

Variant	rs200956
Chromosome Location	chr6:27839746-27839747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:268)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:268 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27838549-27841707	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr6:27838747-27841649	PBDE	blood:	n/a	n/a
3	CTCF	chr6:27839700-27839850	GM12873	blood:	n/a	n/a
4	CTCF	chr6:27839680-27839830	NHEK	skin:	n/a	n/a
5	POLR2A	chr6:27839649-27840255	HUVEC	blood vessel:	n/a	n/a
6	CTCF	chr6:27839680-27839830	GM12870	blood:	n/a	n/a
7	ZBTB33	chr6:27839635-27840177	GM12878	blood:	n/a	n/a
8	CTCF	chr6:27839740-27839890	HBMEC	blood vessel:	n/a	n/a
9	TAF1	chr6:27839495-27840328	H1-hESC	embryonic stem cell:	n/a	n/a
10	CHD1	chr6:27839408-27841329	GM12878	blood:	n/a	n/a
11	SIN3AK20	chr6:27838964-27840391	SK-N-SH	brain:	n/a	n/a
12	ZNF384	chr6:27839677-27840331	GM12878	blood:	n/a	n/a
13	CTCF	chr6:27839671-27839967	MCF-7	breast:	n/a	n/a
14	POLR2A	chr6:27839297-27840460	MCF10A-Er-Src	breast:	n/a	n/a
15	CTCF	chr6:27839673-27840053	MCF-7	breast:	n/a	n/a
16	CTCF	chr6:27839733-27839921	GM10266	blood:	n/a	n/a
17	MAX	chr6:27839358-27840336	NB4	blood:	n/a	n/a
18	MTA3	chr6:27838567-27841844	GM12878	blood:	n/a	n/a
19	REST	chr6:27839741-27840373	H1-neurons	neurons:	n/a	n/a
20	CTCF	chr6:27839686-27840086	GM19238	blood:	n/a	n/a
21	POLR2A	chr6:27839631-27840387	H1-neurons	neurons:	n/a	n/a
22	TAF7	chr6:27839104-27840304	H1-hESC	embryonic stem cell:	n/a	n/a
23	YY1	chr6:27839703-27840287	SK-N-SH_RA	brain:	n/a	n/a
24	SP1	chr6:27839722-27840445	A549	lung:	n/a	chr6:27840162-27840183
25	CTCF	chr6:27839700-27839850	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr6:27838887-27840415	MCF-7	breast:	n/a	n/a
27	YY1	chr6:27839657-27840293	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr6:27839739-27839897	GM10248	blood:	n/a	n/a
29	RELA	chr6:27838795-27841703	GM10847	blood:	n/a	n/a
30	SP1	chr6:27839698-27840431	GM12878	blood:	n/a	chr6:27840162-27840183
31	CHD2	chr6:27839724-27840350	GM12878	blood:	n/a	n/a
32	NFIC	chr6:27839175-27841922	GM12878	blood:	n/a	n/a
33	ZBTB33	chr6:27839174-27840349	A549	lung:	n/a	n/a
34	CTCF	chr6:27839700-27839850	GM12867	blood:	n/a	n/a
35	PAX5	chr6:27839710-27840166	GM12878	blood:	n/a	n/a
36	POU2F2	chr6:27839529-27840298	GM12891	blood:	n/a	n/a
37	CTCF	chr6:27839680-27839830	GM12867	blood:	n/a	n/a
38	RCOR1	chr6:27839697-27840283	GM12878	blood:	n/a	n/a
39	TCF3	chr6:27839309-27840182	GM12878	blood:	n/a	n/a
40	CTCF	chr6:27839686-27839962	GM12892	blood:	n/a	n/a
41	CTCF	chr6:27839740-27839890	AG10803	skin:	n/a	n/a
42	CTCF	chr6:27839740-27839890	HRPEpiC	eye:	n/a	n/a
43	RELA	chr6:27839203-27841750	GM18505	blood:	n/a	n/a
44	YY1	chr6:27839565-27840208	GM12891	blood:	n/a	n/a
45	CTCF	chr6:27839732-27839887	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr6:27839714-27839916	NHEK	skin:	n/a	n/a
47	CTCF	chr6:27839694-27840069	GM19240	blood:	n/a	n/a
48	CTCF	chr6:27839720-27839870	AG04450	lung:	n/a	n/a
49	POLR2A	chr6:27839125-27840442	U87	brain:	n/a	n/a
50	POLR2A	chr6:27838660-27841777	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:26053886..26056754-chr6:27838528..27841562,3	MCF-7	breast:
2	chr6:27098237..27102845-chr6:27835694..27840254,5	MCF-7	breast:
3	chr1:149813872..149815940-chr6:27838697..27841107,2	MCF-7	breast:
4	chr6:26045566..26046278-chr6:27839320..27840308,2	MCF-7	breast:
5	chr6:26044692..26047309-chr6:27838299..27842021,15	MCF-7	breast:
6	chr17:57914621..57917067-chr6:27838760..27840646,2	MCF-7	breast:
7	chr19:10676311..10676946-chr6:27839579..27840253,2	NB4	blood:
8	chr6:27100852..27101558-chr6:27839278..27840055,2	NB4	blood:
9	chr10:77161426..77162368-chr6:27839599..27840288,2	NB4	blood:
10	chr6:26031607..26034880-chr6:27837430..27841431,3	K562	blood:
11	chr6:26044526..26047786-chr6:27838310..27841317,7	MCF-7	breast:
12	chr6:27838398..27840922-chr8:145149536..145152050,2	MCF-7	breast:
13	chr17:57922571..57924385-chr6:27837203..27839996,2	MCF-7	breast:
14	chr1:16839419..16842042-chr6:27838981..27840921,2	MCF-7	breast:
15	chr6:26268562..26271550-chr6:27838233..27840069,2	MCF-7	breast:
16	chr6:27837988..27840286-chr7:80547684..80550334,2	MCF-7	breast:
17	chr12:59313255..59314867-chr6:27838598..27840298,2	MCF-7	breast:
18	chr16:89989067..89989736-chr6:27839677..27840311,2	NB4	blood:
19	chr6:26025188..26029060-chr6:27836295..27841543,4	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H1B	TF binding region
ENSG00000258947	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000220323	Chromatin interaction
ENSG00000261135	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000196532	Chromatin interaction
ENSG00000179091	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000259006	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000075223	Chromatin interaction
ENSG00000139263	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000183558	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000129347	Chromatin interaction
ENSG00000257443	Chromatin interaction
ENSG00000165655	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10484401	0.83[CHD][hapmap]
rs200486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs200502	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs200503	0.89[ASN][1000 genomes]
rs200504	0.85[ASN][1000 genomes]
rs200969	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs200978	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs200991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs200994	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs201000	0.94[ASN][1000 genomes]
rs201001	0.94[ASN][1000 genomes]
rs201004	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[ASN][1000 genomes]
rs573179	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs742047	0.83[CHD][hapmap]
rs9295740	0.89[LWK][hapmap];0.81[MEX][hapmap]
rs9295746	0.83[CHD][hapmap]
rs9461406	0.83[CHD][hapmap]
rs9468220	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
3	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
4	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
5	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs200956	ZSCAN23	cis	cerebellum	SCAN
rs200956	ZNF323	cis	parietal	SCAN
rs200956	NKAPL	cis	parietal	SCAN
rs200956	BTN2A1	cis	parietal	SCAN
rs200956	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs200956	LRRC16A	cis	parietal	SCAN
rs200956	ZNF192	cis	cerebellum	SCAN
rs200956	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs200956	BTN3A2	trans	lymphoblastoid	seeQTL
rs200956	OR2B8P	cis	Thyroid	GTEx
rs200956	AL022393.7	cis	Muscle Skeletal	GTEx
rs200956	BTN3A2	cis	multi-tissue	Pritchard
rs200956	ZKSCAN3	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27838200-27839800	Flanking Active TSS	Dnd41	blood
2	chr6:27838200-27839800	Enhancers	K562	blood
3	chr6:27838200-27842000	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:27838600-27842400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr6:27838800-27840800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:27838800-27841000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:27838800-27841400	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr6:27838800-27842400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:27839000-27839800	Flanking Active TSS	Fetal Thymus	thymus
10	chr6:27839000-27840800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:27839000-27841400	Active TSS	H1 Cell Line	embryonic stem cell
12	chr6:27839000-27841400	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr6:27839000-27841400	Active TSS	Fetal Kidney	kidney
14	chr6:27839000-27841600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:27839000-27842200	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr6:27839000-27842200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:27839000-27842400	Active TSS	Thymus	Thymus
18	chr6:27839000-27842800	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr6:27839200-27839800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:27839200-27839800	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr6:27839200-27839800	Flanking Active TSS	Fetal Intestine Small	intestine
22	chr6:27839200-27839800	Flanking Active TSS	Fetal Stomach	stomach
23	chr6:27839200-27839800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr6:27839200-27839800	Flanking Active TSS	NH-A	brain
25	chr6:27839200-27840000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr6:27839200-27840000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:27839200-27840000	Flanking Active TSS	Fetal Muscle Trunk	muscle
28	chr6:27839200-27840000	Flanking Active TSS	HMEC	breast
29	chr6:27839200-27840000	Flanking Active TSS	HUVEC	blood vessel
30	chr6:27839200-27840000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr6:27839200-27840600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr6:27839200-27840800	Active TSS	NHLF	lung
33	chr6:27839200-27841400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:27839200-27841400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:27839200-27841600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:27839200-27841600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:27839200-27841800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:27839200-27842000	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr6:27839200-27842200	Active TSS	H9 Cell Line	embryonic stem cell
40	chr6:27839400-27839800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:27839400-27839800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:27839400-27839800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr6:27839400-27839800	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr6:27839400-27839800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr6:27839400-27839800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr6:27839400-27839800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr6:27839400-27839800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr6:27839400-27839800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr6:27839400-27839800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr6:27839400-27839800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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