Variant report

Variant	rs3132650
Chromosome Location	chr6:30312176-30312177
allele	C/T
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	chr6:30312003-30313348	K562	blood:	n/a	n/a
2	JUND	chr6:30311935-30313175	K562	blood:	n/a	chr6:30312344-30312356 chr6:30312183-30312194 chr6:30312185-30312194 chr6:30312181-30312192
3	ELF1	chr6:30312100-30313243	K562	blood:	n/a	chr6:30312389-30312400
4	NR2F2	chr6:30311833-30313285	K562	blood:	n/a	n/a
5	TAF1	chr6:30311939-30312403	K562	blood:	n/a	n/a
6	POLR2A	chr6:30311907-30313534	K562	blood:	n/a	n/a
7	JUN	chr6:30311147-30314064	K562	blood:	n/a	chr6:30312344-30312356 chr6:30312185-30312194 chr6:30312181-30312192
8	MAX	chr6:30311993-30312507	K562	blood:	n/a	n/a
9	BHLHE40	chr6:30312009-30312423	K562	blood:	n/a	n/a
10	POLR2A	chr6:30311910-30312431	K562	blood:	n/a	n/a
11	MAX	chr6:30312016-30313487	K562	blood:	n/a	chr6:30312850-30312860
12	RCOR1	chr6:30312007-30312458	K562	blood:	n/a	n/a
13	JUND	chr6:30312138-30312227	HepG2	liver:	n/a	chr6:30312183-30312194 chr6:30312185-30312194 chr6:30312181-30312192
14	HDAC2	chr6:30311972-30312371	K562	blood:	n/a	n/a
15	FOSL1	chr6:30311881-30312364	K562	blood:	n/a	chr6:30312344-30312356 chr6:30312185-30312194 chr6:30312181-30312192 chr6:30312183-30312194
16	NR2F2	chr6:30311836-30312823	K562	blood:	n/a	n/a
17	TEAD4	chr6:30311911-30312489	K562	blood:	n/a	n/a
18	MAZ	chr6:30311997-30313495	K562	blood:	n/a	chr6:30312850-30312860
19	HMGN3	chr6:30312053-30312403	K562	blood:	n/a	n/a
20	ATF3	chr6:30311950-30312394	K562	blood:	n/a	n/a
21	JUN	chr6:30312001-30312403	K562	blood:	n/a	chr6:30312344-30312356 chr6:30312185-30312194 chr6:30312181-30312192
22	POLR2A	chr6:30311254-30314649	HepG2	liver:	n/a	n/a
23	FOSL1	chr6:30311979-30312353	K562	blood:	n/a	chr6:30312185-30312194 chr6:30312181-30312192 chr6:30312183-30312194
24	ZNF384	chr6:30312122-30313274	K562	blood:	n/a	n/a
25	PML	chr6:30311947-30313410	K562	blood:	n/a	n/a
26	TBP	chr6:30312102-30313346	K562	blood:	n/a	n/a
27	CUX1	chr6:30311927-30312881	K562	blood:	n/a	n/a
28	CBX3	chr6:30311850-30313408	K562	blood:	n/a	n/a
29	UBTF	chr6:30312002-30312271	K562	blood:	n/a	n/a
30	EP300	chr6:30311928-30313171	K562	blood:	n/a	chr6:30312725-30312733 chr6:30312184-30312193 chr6:30312391-30312400
31	STAT5A	chr6:30311960-30313188	K562	blood:	n/a	chr6:30312896-30312908
32	POLR2A	chr6:30311900-30312248	GM12878	blood:	n/a	n/a
33	ZBTB7A	chr6:30311974-30312531	K562	blood:	n/a	n/a
34	CCNT2	chr6:30312022-30312395	K562	blood:	n/a	n/a
35	POLR2A	chr6:30311955-30313405	K562	blood:	n/a	n/a
36	TBL1XR1	chr6:30312096-30312443	K562	blood:	n/a	n/a
37	POLR2A	chr6:30311633-30313565	K562	blood:	n/a	n/a
38	HCFC1	chr6:30312090-30313727	Hela-S3	cervix:	n/a	n/a
39	HEY1	chr6:30312032-30312386	K562	blood:	n/a	n/a
40	TAL1	chr6:30312019-30312361	K562	blood:	n/a	n/a
41	TEAD4	chr6:30311927-30313602	K562	blood:	n/a	n/a
42	ZBTB7A	chr6:30312060-30312384	K562	blood:	n/a	n/a
43	POLR2A	chr6:30311900-30313471	K562	blood:	n/a	n/a
44	CEBPD	chr6:30311955-30313226	K562	blood:	n/a	n/a
45	JUN	chr6:30311986-30312372	K562	blood:	n/a	chr6:30312344-30312356 chr6:30312185-30312194 chr6:30312181-30312192
46	TBL1XR1	chr6:30312071-30313224	K562	blood:	n/a	n/a
47	MAFK	chr6:30311930-30313008	K562	blood:	n/a	n/a
48	RCOR1	chr6:30312067-30313134	K562	blood:	n/a	n/a
49	POLR2A	chr6:30311875-30313217	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30225542..30228363-chr6:30311426..30313496,2	MCF-7	breast:
2	chr6:30311691..30313259-chr6:30331666..30334647,2	K562	blood:
3	chr6:30178310..30184484-chr6:30311860..30320436,13	MCF-7	breast:
4	chr6:30261501..30265546-chr6:30310228..30314438,4	K562	blood:
5	chr6:30226682..30228906-chr6:30311932..30314057,2	MCF-7	breast:
6	chr6:30180733..30183619-chr6:30310467..30312981,3	MCF-7	breast:
7	chr6:30311779..30313708-chr6:30523664..30525763,2	MCF-7	breast:
8	chr6:30293058..30297784-chr6:30308514..30315279,24	MCF-7	breast:
9	chr6:30312149..30313971-chr6:30583567..30587070,3	K562	blood:
10	chr6:30312087..30314441-chr6:30330908..30332882,2	MCF-7	breast:

Variant related genes	Relation type
RPP21	TF binding region
ENSG00000231074	Chromatin interaction
ENSG00000243753	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000236405	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000234127	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000270604	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204599	Chromatin interaction
ENSG00000248167	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs2844770	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2844771	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2844773	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs3094070	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3094071	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3094072	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3094073	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3094074	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3094076	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3094077	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3094629	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3094630	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3094632	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3129697	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3129699	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3129700	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3129701	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3129702	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3129703	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3129704	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3129705	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3129706	0.98[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs3129707	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3129708	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3129831	0.98[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3129832	0.98[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3129835	0.98[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs3129836	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3129837	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3129840	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130398	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3130400	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3130401	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3130403	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3130404	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3130405	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3132655	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3132656	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3132657	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3132658	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3132659	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs885916	0.80[EUR][1000 genomes]
rs9261629	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9261630	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9261636	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3132650	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30295600-30312600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:30295600-30312600	Weak transcription	Right Atrium	heart
3	chr6:30295600-30313000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:30295800-30312400	Weak transcription	Fetal Heart	heart
5	chr6:30295800-30312400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:30298600-30312600	Weak transcription	Fetal Brain Male	brain
7	chr6:30304000-30312600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:30304400-30312400	Weak transcription	A549	lung
9	chr6:30306000-30312400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:30306400-30312600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:30306600-30312600	Weak transcription	HUVEC	blood vessel
12	chr6:30308200-30312400	Weak transcription	GM12878-XiMat	blood
13	chr6:30308600-30312400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:30309200-30312600	Weak transcription	HSMM	muscle
15	chr6:30309400-30312200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:30309800-30312200	Weak transcription	Hela-S3	cervix
17	chr6:30309800-30312400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr6:30309800-30312400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:30309800-30312400	Weak transcription	Psoas Muscle	Psoas
20	chr6:30310000-30312400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:30310000-30312400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr6:30310000-30312400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:30310000-30312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:30310000-30312400	Weak transcription	Colon Smooth Muscle	Colon
25	chr6:30310000-30312400	Weak transcription	Fetal Lung	lung
26	chr6:30310000-30312400	Weak transcription	NH-A	brain
27	chr6:30310000-30312600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr6:30310000-30312600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr6:30310000-30312600	Weak transcription	HMEC	breast
30	chr6:30310000-30312800	Weak transcription	Esophagus	oesophagus
31	chr6:30310000-30313000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:30310200-30312200	Weak transcription	Dnd41	blood
33	chr6:30310200-30312200	Weak transcription	NHLF	lung
34	chr6:30310200-30312400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:30310200-30312400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr6:30310200-30312400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:30310200-30312400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:30310200-30312400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:30310200-30312400	Weak transcription	Brain Angular Gyrus	brain
40	chr6:30310200-30312400	Weak transcription	Colonic Mucosa	Colon
41	chr6:30310200-30312400	Weak transcription	Fetal Kidney	kidney
42	chr6:30310200-30312400	Weak transcription	Fetal Thymus	thymus
43	chr6:30310200-30312400	Weak transcription	Pancreas	Pancrea
44	chr6:30310200-30312400	Weak transcription	Small Intestine	intestine
45	chr6:30310200-30312600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr6:30310200-30312600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr6:30310200-30312600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:30310200-30312600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:30310200-30312600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:30310200-30312600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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