Variant report

Variant	rs198810
Chromosome Location	chr6:26128618-26128619
allele	A/G
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	NR2F2	chr6:26127734-26129124	K562	blood:	n/a	n/a
2	POLR2A	chr6:26128407-26128857	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:26128424-26128664	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:26128206-26129197	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr6:26128357-26129622	K562	blood:	n/a	n/a
6	TBL1XR1	chr6:26128548-26128910	K562	blood:	n/a	n/a
7	POLR2A	chr6:26128421-26128705	H1-hESC	embryonic stem cell:	n/a	n/a
8	PML	chr6:26122206-26129108	K562	blood:	n/a	n/a
9	POLR2A	chr6:26128332-26128983	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr6:26128410-26128707	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr6:26112014-26135800	K562	blood:	n/a	n/a
12	CEBPB	chr6:26128557-26129053	K562	blood:	n/a	chr6:26129030-26129043 chr6:26128738-26128749
13	CEBPD	chr6:26128278-26129170	K562	blood:	n/a	n/a
14	MXI1	chr6:26128537-26128970	K562	blood:	n/a	n/a
15	CBX3	chr6:26128411-26128872	K562	blood:	n/a	n/a
16	POLR2A	chr6:26128292-26128744	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:26128366-26128743	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr6:26120221-26136970	K562	blood:	n/a	n/a
19	HEY1	chr6:26128416-26128985	K562	blood:	n/a	n/a
20	POLR2A	chr6:26128487-26128831	MCF-7	breast:	n/a	n/a
21	POLR2A	chr6:26121000-26129264	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr6:26121435-26133623	K562	blood:	n/a	n/a
23	POLR2A	chr6:26128576-26128638	ProgFib	skin:	n/a	n/a
24	BCLAF1	chr6:26120463-26129092	K562	blood:	n/a	chr6:26126779-26126788 chr6:26122722-26122731 chr6:26125896-26125905
25	HEY1	chr6:26121111-26129034	K562	blood:	n/a	n/a
26	POLR2A	chr6:26122559-26128971	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr6:26128501-26128637	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:26119863..26128842-chr6:27096583..27102911,26	K562	blood:
2	chr6:26017750..26036418-chr6:26116875..26130553,65	MCF-7	breast:
3	chr1:11967127..11969699-chr6:26127396..26129327,2	K562	blood:

Variant related genes	Relation type
HIST1H2BC	TF binding region
ENSG00000196176	Chromatin interaction
ENSG00000124610	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000137259	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10425	0.84[CHD][hapmap];0.88[GIH][hapmap]
rs1068554	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs115810	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12346	0.80[CEU][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.84[TSI][hapmap];0.82[ASN][1000 genomes]
rs129129	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs1540275	0.86[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap]
rs1540276	0.86[CHB][hapmap]
rs198801	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs198815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198818	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198820	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198834	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198845	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs198847	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs198848	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs198849	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs198850	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs198852	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs198853	0.89[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs199737	0.86[CHB][hapmap]
rs199739	0.86[CHB][hapmap]
rs199741	0.86[CHB][hapmap]
rs199750	0.88[CHD][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap]
rs199751	0.86[CHB][hapmap]
rs199752	0.88[CHD][hapmap];0.90[MEX][hapmap]
rs199753	0.86[CHB][hapmap]
rs199754	0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap]
rs2032447	0.80[CHD][hapmap];0.84[GIH][hapmap]
rs2213284	0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap]
rs2230655	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap]
rs4401650	0.84[CHD][hapmap];0.86[GIH][hapmap];0.90[MEX][hapmap]
rs442601	0.86[CHB][hapmap]
rs6901039	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs6922788	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs7756117	0.84[CHD][hapmap];0.84[GIH][hapmap]
rs807212	0.86[CHB][hapmap]
rs807214	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv1028456	chr6:25984457-26174993	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
8	nsv538165	chr6:25984457-26174993	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
9	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
10	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
11	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
12	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
13	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
14	nsv1025493	chr6:26026870-26223838	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1001 gene(s)	inside rSNPs	diseases
15	nsv1023979	chr6:26026870-26287399	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1113 gene(s)	inside rSNPs	diseases
16	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
17	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
18	nsv482348	chr6:26082709-26261136	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	799 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs198810	HIST1H4I	cis	cerebellum	SCAN
rs198810	HIST1H2BB	cis	parietal	SCAN
rs198810	HIST1H2AA	cis	parietal	SCAN
rs198810	HIST1H2BC	cis	cerebellum	SCAN
rs198810	BTN2A2	cis	lymphoblastoid	seeQTL
rs198810	HIST1H2AJ	cis	parietal	SCAN
rs198810	HIST1H2BM	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26124600-26134200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:26125400-26129200	Transcr. at gene 5' and 3'	K562	blood
3	chr6:26126400-26129000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:26126400-26130000	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
5	chr6:26126600-26128800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
6	chr6:26126600-26129600	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
7	chr6:26126800-26128800	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr6:26126800-26129000	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
9	chr6:26127000-26131200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:26127000-26131200	Weak transcription	Lung	lung
11	chr6:26127000-26141600	Weak transcription	Gastric	stomach
12	chr6:26127200-26129000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:26127200-26130000	Weak transcription	Small Intestine	intestine
14	chr6:26127200-26131200	Weak transcription	Esophagus	oesophagus
15	chr6:26127200-26139400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:26127200-26139600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:26127400-26129000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr6:26127400-26129000	Transcr. at gene 5' and 3'	Liver	Liver
19	chr6:26127400-26131400	Weak transcription	HSMM	muscle
20	chr6:26127600-26129000	Enhancers	Fetal Lung	lung
21	chr6:26127600-26129000	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
22	chr6:26127600-26129600	Weak transcription	Colonic Mucosa	Colon
23	chr6:26127600-26129800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:26127600-26138800	Weak transcription	Aorta	Aorta
25	chr6:26127600-26138800	Weak transcription	Ovary	ovary
26	chr6:26127800-26128800	Enhancers	Fetal Brain Male	brain
27	chr6:26127800-26128800	Enhancers	Spleen	Spleen
28	chr6:26127800-26128800	Enhancers	HMEC	breast
29	chr6:26127800-26129000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:26127800-26129000	Genic enhancers	Brain Anterior Caudate	brain
31	chr6:26127800-26129000	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr6:26127800-26129000	Enhancers	Right Atrium	heart
33	chr6:26127800-26129600	Weak transcription	Psoas Muscle	Psoas
34	chr6:26127800-26129800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr6:26127800-26129800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:26127800-26130000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr6:26127800-26130200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr6:26127800-26130600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:26127800-26130600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
40	chr6:26127800-26130800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr6:26127800-26131200	Weak transcription	Right Ventricle	heart
42	chr6:26127800-26131800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr6:26127800-26132200	Strong transcription	Fetal Muscle Leg	muscle
44	chr6:26127800-26132400	Weak transcription	Fetal Heart	heart
45	chr6:26127800-26134200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr6:26127800-26136200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:26127800-26138600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr6:26127800-26140200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr6:26127800-26141800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:26127800-26143000	Weak transcription	NH-A	brain

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